RetrogeneDB ID: retro_hsap_4883

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: X:100110282..100110848(-)
• Located in intron of: ENSG00000007952

Retrocopy information

• Ensembl ID: ENSG00000239345
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA1
• Ensembl ID: ENSG00000135486
• Aliases: HNRNPA1, ALS19, ALS20, HNRPA1, HNRPA1L3, IBMPFD3, hnRNP A1, hnRNP-A1
• Description: heterogeneous nuclear ribonucleoprotein A1 [Source:HGNC Symbol;Acc:5031]

Sequence

>retro_hsap_4883
GAAGTTAGGAAAGCCCTGTCAAAGCAAGAGATGGCTAGTGCTTCATCCAGCCAAAGAGGTCGAAGTGGTCGTGGAGGTGG
TTTTGGTGGGAATGAAAACTTTGGTTGTGGAGGAAACTTCAGTGGTCATGGTGGCTTTGGTGGCAGCCATGATGGTGGTG
GATATGGTGGCAGTGGGGATGGCTATAATGGATTTGGTAATGATGGTGGTTATCCAGGAGGCGGCCCTGGTTACTCTGGA
GGAAGCAGAGGCTATGGAAGTGGTGGACAGGGTTGTGGAAATCAGGACAGTGGCTATGGCAGGAGTGGCAGCTATGACAG
CTGTAACAAGGGAGGCAGAGGCGGCTTTGGCAGTGGTAGTGGAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTG
GCAATTACAACAATCAGTATTCAAATTTTGGACCCATGAAGGGAGGAAACTTTGGGGCAGACGCTCTGGCCCCTAGGGTG
ATGGAGGCCAATACTTTGCCAAACCACCAAACCACAGTGGCTATGGCGGTTCCAGTAGCAGCAGTAGCTATGGCAGTGGC
AGAAGA

Alignment

ORF - retro_hsap_4883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.63 %
• Parental protein coverage: 50.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EMASASSSQRGRSGSGNFGG--GRGGGFGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGG
          E...A.S.Q...S.S....G..GRGGGFGGN.NFG.GGNFSG...................YNGFGNDGG
Retrocopy EVRKALSKQEMASASSSQRGRSGRGGGFGGNENFGCGGNFSGXXXXXXXXXXXXXXXXXXXYNGFGNDGG

Parental  YGGGGPGYSGGSRGYGSGGQGYGNQGSGYGGSGSYDSYNNGGGGGFGGGSGSNFGGGGSYNDFGNYNNQS
          Y.GGGPGYSGGSRGYGSGGQG.GNQ.SGYG.SGSYDS.N.GG.GGFG.GSGSNFGGGGSYNDFGNYNNQ.
Retrocopy YPGGGPGYSGGSRGYGSGGQGCGNQDSGYGRSGSYDSCNKGGRGGFGSGSGSNFGGGGSYNDFGNYNNQY

Parental  SNFGPMKGGNFG-GRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRR
          SNFGPMKGGNFG.GR.SGP.G.GGQYFAKP.N..GYGGSSSSSSYGSGRR
Retrocopy SNFGPMKGGNFG<GRRSGP*GDGGQYFAKPPNHSGYGGSSSSSSYGSGRR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	0.12 RPM	775.80 RPM
bodymap2_adrenal	0.20 RPM	1006.81 RPM
bodymap2_brain	0.09 RPM	373.10 RPM
bodymap2_breast	0.02 RPM	438.74 RPM
bodymap2_colon	0.19 RPM	730.72 RPM
bodymap2_heart	0.00 RPM	200.75 RPM
bodymap2_kidney	0.00 RPM	336.99 RPM
bodymap2_liver	0.00 RPM	126.11 RPM
bodymap2_lung	0.00 RPM	423.66 RPM
bodymap2_lymph_node	0.00 RPM	358.27 RPM
bodymap2_ovary	0.27 RPM	1611.66 RPM
bodymap2_prostate	0.00 RPM	619.57 RPM
bodymap2_skeletal_muscle	0.05 RPM	321.98 RPM
bodymap2_testis	0.06 RPM	521.76 RPM
bodymap2_thyroid	0.08 RPM	609.76 RPM
bodymap2_white_blood_cells	0.00 RPM	596.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_4883 was not detected

EST

No EST(s) were mapped for retro_hsap_4883 retrocopy.

TSS

No TSS is located nearby retro_hsap_4883 retrocopy 5' end.

Lab

retro_hsap_4883 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4883 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 215 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001553	20 retrocopies	retro_btau_1019, retro_btau_1065, retro_btau_1268, retro_btau_1378, retro_btau_1379, retro_btau_1437, retro_btau_1455, retro_btau_1657, retro_btau_1673, retro_btau_283, retro_btau_337, retro_btau_403, retro_btau_462, retro_btau_516, retro_btau_519, retro_btau_589, retro_btau_602, retro_btau_677, retro_btau_715, retro_btau_822,
Cavia porcellus	ENSCPOG00000020972	1 retrocopy	retro_cpor_1078,
Equus caballus	ENSECAG00000008676	1 retrocopy	retro_ecab_74,
Felis catus	ENSFCAG00000010150	9 retrocopies	retro_fcat_1574, retro_fcat_1742, retro_fcat_1867, retro_fcat_382, retro_fcat_474, retro_fcat_712, retro_fcat_781, retro_fcat_844, retro_fcat_888,
Homo sapiens	ENSG00000135486	57 retrocopies	retro_hsap_1021, retro_hsap_1042, retro_hsap_1082, retro_hsap_1240, retro_hsap_1276, retro_hsap_1282, retro_hsap_1287, retro_hsap_1481, retro_hsap_158, retro_hsap_1584, retro_hsap_1613, retro_hsap_1638, retro_hsap_1711, retro_hsap_1899, retro_hsap_1933, retro_hsap_2002, retro_hsap_2029, retro_hsap_2091, retro_hsap_2096, retro_hsap_2197, retro_hsap_2347, retro_hsap_2379, retro_hsap_2636, retro_hsap_2640, retro_hsap_2668, retro_hsap_2718, retro_hsap_2857, retro_hsap_291, retro_hsap_2917, retro_hsap_2944, retro_hsap_3049, retro_hsap_3055, retro_hsap_332, retro_hsap_3343, retro_hsap_3393, retro_hsap_3432, retro_hsap_3439, retro_hsap_3449, retro_hsap_3549, retro_hsap_3745, retro_hsap_3756, retro_hsap_3757, retro_hsap_394, retro_hsap_3979, retro_hsap_4011, retro_hsap_4084, retro_hsap_414, retro_hsap_4218, retro_hsap_4282, retro_hsap_437, retro_hsap_4747, retro_hsap_482, retro_hsap_4883 , retro_hsap_668, retro_hsap_84, retro_hsap_845, retro_hsap_924,
Homo sapiens	ENSG00000138668	1 retrocopy	retro_hsap_4689,
Homo sapiens	ENSG00000170144	11 retrocopies	retro_hsap_1117, retro_hsap_1274, retro_hsap_1572, retro_hsap_209, retro_hsap_2194, retro_hsap_2664, retro_hsap_2951, retro_hsap_34, retro_hsap_4764, retro_hsap_665, retro_hsap_862,
Homo sapiens	ENSG00000197451	1 retrocopy	retro_hsap_962,
Gorilla gorilla	ENSGGOG00000003040	6 retrocopies	retro_ggor_1006, retro_ggor_1010, retro_ggor_1221, retro_ggor_1738, retro_ggor_2041, retro_ggor_950,
Mustela putorius furo	ENSMPUG00000004620	1 retrocopy	retro_mputfur_34,
Mustela putorius furo	ENSMPUG00000005735	2 retrocopies	retro_mputfur_1378, retro_mputfur_653,
Mus musculus	ENSMUSG00000046434	3 retrocopies	retro_mmus_1861, retro_mmus_410, retro_mmus_543,
Nomascus leucogenys	ENSNLEG00000017659	34 retrocopies	retro_nleu_1011, retro_nleu_1090, retro_nleu_1257, retro_nleu_130, retro_nleu_132, retro_nleu_1497, retro_nleu_1630, retro_nleu_1648, retro_nleu_166, retro_nleu_167, retro_nleu_1695, retro_nleu_1739, retro_nleu_1774, retro_nleu_1802, retro_nleu_1875, retro_nleu_190, retro_nleu_2040, retro_nleu_2222, retro_nleu_2304, retro_nleu_2324, retro_nleu_2378, retro_nleu_2690, retro_nleu_2742, retro_nleu_2852, retro_nleu_32, retro_nleu_366, retro_nleu_458, retro_nleu_587, retro_nleu_601, retro_nleu_645, retro_nleu_648, retro_nleu_708, retro_nleu_825, retro_nleu_987,
Oryctolagus cuniculus	ENSOCUG00000013350	1 retrocopy	retro_ocun_1675,
Oreochromis niloticus	ENSONIG00000012248	1 retrocopy	retro_onil_38,
Ochotona princeps	ENSOPRG00000006107	10 retrocopies	retro_opri_1183, retro_opri_338, retro_opri_349, retro_opri_424, retro_opri_456, retro_opri_597, retro_opri_753, retro_opri_782, retro_opri_79, retro_opri_843,
Pteropus vampyrus	ENSPVAG00000000322	9 retrocopies	retro_pvam_1133, retro_pvam_1230, retro_pvam_1313, retro_pvam_1370, retro_pvam_196, retro_pvam_300, retro_pvam_453, retro_pvam_643, retro_pvam_859,
Rattus norvegicus	ENSRNOG00000036839	17 retrocopies	retro_rnor_1001, retro_rnor_1322, retro_rnor_1658, retro_rnor_1770, retro_rnor_1786, retro_rnor_1846, retro_rnor_1987, retro_rnor_2194, retro_rnor_2482, retro_rnor_2551, retro_rnor_2619, retro_rnor_2657, retro_rnor_2881, retro_rnor_2944, retro_rnor_2945, retro_rnor_2965, retro_rnor_2969,
Tupaia belangeri	ENSTBEG00000008238	30 retrocopies	retro_tbel_1219, retro_tbel_156, retro_tbel_162, retro_tbel_1643, retro_tbel_1830, retro_tbel_1967, retro_tbel_2192, retro_tbel_2195, retro_tbel_2211, retro_tbel_2330, retro_tbel_261, retro_tbel_2666, retro_tbel_2673, retro_tbel_2703, retro_tbel_276, retro_tbel_2774, retro_tbel_2787, retro_tbel_2970, retro_tbel_3473, retro_tbel_3976, retro_tbel_3995, retro_tbel_4266, retro_tbel_4271, retro_tbel_453, retro_tbel_4653, retro_tbel_4729, retro_tbel_692, retro_tbel_70, retro_tbel_79, retro_tbel_839,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.09 RPM
CEU_NA11843	0.28 RPM
CEU_NA11930	0.10 RPM
CEU_NA12004	0.38 RPM
CEU_NA12400	0.21 RPM
CEU_NA12751	0.17 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.09 RPM
CEU_NA12872	0.35 RPM
CEU_NA12873	0.22 RPM
FIN_HG00183	0.16 RPM
FIN_HG00277	0.37 RPM
FIN_HG00315	0.22 RPM
FIN_HG00321	0.30 RPM
FIN_HG00328	0.26 RPM
FIN_HG00338	0.28 RPM
FIN_HG00349	0.11 RPM
FIN_HG00375	0.24 RPM
FIN_HG00377	0.33 RPM
FIN_HG00378	0.21 RPM
GBR_HG00099	0.23 RPM
GBR_HG00111	0.26 RPM
GBR_HG00114	0.26 RPM
GBR_HG00119	0.24 RPM
GBR_HG00131	0.23 RPM
GBR_HG00133	0.27 RPM
GBR_HG00134	0.20 RPM
GBR_HG00137	0.16 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.13 RPM
TSI_NA20512	0.23 RPM
TSI_NA20513	0.53 RPM
TSI_NA20518	0.53 RPM
TSI_NA20532	0.07 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.23 RPM
TSI_NA20765	0.21 RPM
TSI_NA20771	0.17 RPM
TSI_NA20786	0.13 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.24 RPM
YRI_NA18907	0.14 RPM
YRI_NA18916	0.25 RPM
YRI_NA19093	0.10 RPM
YRI_NA19099	0.13 RPM
YRI_NA19114	0.13 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	0.17 RPM
YRI_NA19214	0.22 RPM
YRI_NA19223	0.22 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).