Duplicate transcripts for genes in exons_nirvana2010_no_PAR_Y

[jethror1]

2 entries found for gene LARGE1 in exons_nirvana which point to LARGE1 (new symbol) and LARGE (old symbol) in nirvana_genes2transcripts:

jethro@jethro-T490:~$ grep LARGE Projects/eggd_001_Reference/dynamic_files/nirvana_genes2transcripts/nirvana_genes2transcripts_2010_201109
LARGE1 NM_004737.4
LARGE NM_133642.3

jethro@jethro-T490:~$ grep NM_004737.4 ~/Projects/app_testing/generate_bed_data/exons_nirvana2010_no_PAR_Y.tsv
22 33670407 33670615 LARGE1 NM_004737.4 16
22 33673040 33673246 LARGE1 NM_004737.4 15
22 33679182 33679339 LARGE1 NM_004737.4 14
22 33700209 33700498 LARGE1 NM_004737.4 13
22 33712065 33712239 LARGE1 NM_004737.4 12
22 33733626 33733792 LARGE1 NM_004737.4 11
22 33777899 33778035 LARGE1 NM_004737.4 10
22 33780172 33780295 LARGE1 NM_004737.4 9
22 33828141 33828256 LARGE1 NM_004737.4 8
22 33960828 33961010 LARGE1 NM_004737.4 7
22 34000415 34000549 LARGE1 NM_004737.4 6
22 34022222 34022315 LARGE1 NM_004737.4 5
22 34046347 34046659 LARGE1 NM_004737.4 4
22 34157352 34157468 LARGE1 NM_004737.4 3

jethro@jethro-T490:~$ grep NM_133642.3 ~/Projects/app_testing/generate_bed_data/exons_nirvana2010_no_PAR_Y.tsv
22 33670407 33670615 LARGE1 NM_133642.3 15
22 33673040 33673246 LARGE1 NM_133642.3 14
22 33679182 33679339 LARGE1 NM_133642.3 13
22 33700209 33700498 LARGE1 NM_133642.3 12
22 33712065 33712239 LARGE1 NM_133642.3 11
22 33733626 33733792 LARGE1 NM_133642.3 10
22 33777899 33778035 LARGE1 NM_133642.3 9
22 33780172 33780295 LARGE1 NM_133642.3 8
22 33828141 33828256 LARGE1 NM_133642.3 7
22 33960828 33961010 LARGE1 NM_133642.3 6
22 34000415 34000549 LARGE1 NM_133642.3 5
22 34022222 34022315 LARGE1 NM_133642.3 4
22 34046347 34046659 LARGE1 NM_133642.3 3
22 34157352 34157468 LARGE1 NM_133642.3 2

[jethror1]

gene => gene symbol in g2t
new_symbol => returned from HGNC
exists => new symbol already in g2t
tx_new_symbol => transcript for gene is assigned to new symbol in exons_nirvana
gene_in_panel => gene in a current gemini panel
new_in_panel => new symbol in a current gemini panel

`	gene	new_symbol	exists	tx_new_symbol	gene_in_panel	new_in_panel
0	AARS	AARS1	False	False	True	False
1	ADCK3	COQ8A	True	True	False	True
2	APOPT1	COA8	False	False	True	False
3	ARMC4	ODAD2	False	False	True	False
4	ARSE	ARSL	False	False	True	False
5	B3GALTL	B3GLCT	True	True	False	True
6	BRF1	ZFP36L1	False	False	True	False
7	C2ORF71	PCARE	False	False	True	False
8	C4ORF26	ODAPH	False	False	True	False
9	C5ORF42	CPLANE1	False	False	True	False
10	C10ORF2	TWNK	True	True	False	True
11	C10ORF11	LRMDA	True	True	True	False
12	C21ORF2	CFAP410	False	False	True	False
13	CASC5	KNL1	True	True	False	True
14	CCDC114	ODAD1	False	False	True	False
15	CCDC151	ODAD3	False	False	True	False
16	CDH3	CDH15	True	False	True	True
17	CECR1	ADA2	True	True	False	True
18	COL4A3BP	CERT1	False	False	True	False
19	DARS	DARS1	False	False	True	False
20	DFNA5	GSDME	True	True	False	True
21	DFNB31	WHRN	True	True	False	True
22	DFNB59	PJVK	True	True	False	True
23	DIRC2	SLC49A4	False	False	False	False
24	DLG3	MPP3	False	False	True	False
25	DLG4	LLGL1	False	False	True	False
26	DSC3	DSC2	True	False	True	True
27	DYX1C1	DNAAF4	True	True	False	True
28	ERF	ETF1	False	False	True	False
29	FAM58A	CCNQ	True	True	False	True
30	FAM134B	RETREG1	True	True	False	True
31	G6PC	G6PC1	False	False	True	False
32	GARS	GARS1	False	False	True	False
33	GIF	CBLIF	False	False	True	False
34	GPR56	ADGRG1	True	True	False	True
35	GPR98	ADGRV1	True	True	False	True
36	GRIK2	GRIK5	False	False	True	False
37	GSS	PRNP	True	False	True	True
38	GUCY1A3	GUCY1A1	False	False	False	False
39	HARS2	DTD1	False	False	True	False
40	HARS	HARS1	False	False	True	False
41	HEATR2	DNAAF5	True	True	False	True
42	HFE2	HJV	True	True	True	True
43	HTT	SLC6A4	False	False	False	False
44	ICK	CILK1	False	False	True	False
45	IKBKAP	ELP1	True	True	False	True
46	IMPAD1	BPNT2	False	False	True	False
47	INPP5E	PMPCA	False	False	True	False
48	ISPD	CRPPA	False	False	True	False
49	KAL1	ANOS1	True	True	False	True
50	KARS	KARS1	False	False	True	False
51	KCNE1L	KCNE5	True	True	False	True
52	KIAA0196	WASHC5	True	True	False	True
53	KIAA0226	RUBCN	True	True	False	True
54	KIAA1279	KIFBP	False	False	False	False
55	KIAA2022	NEXMIF	True	True	False	True
56	KIF1BP	KIFBP	False	False	True	False
57	KRT6C	KRT6A	True	False	True	True
58	LAMB2	LAMC1	False	False	True	False
59	LARGE	LARGE1	True	True	False	True
60	LEPRE1	P3H1	True	True	False	True
61	LOR	LORICRIN	False	False	True	False
62	LTBP2	LTBP3	True	False	True	True
63	LTBP3	LTBP2	True	False	True	True
64	MKL1	MRTFA	False	False	True	False
65	MRE11A	MRE11	True	True	True	True
66	MTTP	MT-TP	False	False	True	False
67	MUT	MMUT	False	False	True	False
68	PARK2	PRKN	True	True	False	True
69	PTRF	CAVIN1	True	True	False	True
70	PVRL4	NECTIN4	True	True	False	True
71	SC5DL	SC5D	True	True	False	True
72	SEPN1	SELENON	True	True	False	True
73	SEPT9	SEPTIN9	False	False	True	False
74	SHFM1	SEM1	True	True	False	False
75	SLC6A5	SLC6A2	False	False	True	False
76	SPG20	SPART	True	True	False	True
77	TCF3	TCF7L1	False	False	True	False
78	TCF4	TCF7L2	False	False	True	False
79	TMEM5	RXYLT1	True	True	True	True
80	TMEM173	STING1	False	False	True	False
81	TRAP1	HSP90B2P	False	False	False	False
82	TUBB	TUBB2A	True	False	True	True
83	VARS2	VARS1	False	False	True	False
84	WDR11	PHIP	True	False	True	True
85	WDR34	DYNC2I2	False	False	True	False
86	WDR60	DYNC2I1	False	False	True	False
87	WHSC1	NSD2	True	True	False	True
88	WISP3	CCN6	False	False	False	False
89	YARS	YARS1	False	False	True	False