RetrogeneDB ID: retro_hsap_1638

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 16:51679728..51680688(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224578
• 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_1638
ATGTCTAAGTCAGAGTCTCCTAAAGAGCCCGAACAGCTGAGGAAGCTCTTCATTGGAGGGTTGAGCTTTGAAACAACTGA
TGAGAGCCTGAGGAGCCATTTTGAGCAATGGGGAACGCTCACGGACTGTGTGGTAATGAGAGATCCAAACACGAAGCGCT
CCAGGGGCTTTGGGTTTGTCACATATGCCACTGTGGAGGAGGTGGATGCAGCTATGAATGCAAGGCCACACAAGGTGGAT
GGAAGAGTTGTGGAACCAAAGAGAGCTGTCTCCAGAGAAGATTCTCAAAGACCAGATGCCCACTTAACTGTGAAAAAGAT
ATTTGTTGGTGGCATTAAAGAAGACACTGAAGAACATCACCTAAGAGATTATTTTGAACAGTATGGAAAAATTGAAGTGA
TTGAAATCATGACTGACAGAGGCAGTGGCAAGAAAAGGGGCTTTGCCTTTGTAACCTTTGACGACCATGACTCCGTGGAT
AAGATTGTCATTCAGAAATACCATACTGTGAATGGCCACAACTGTGAAGTTAGAAAAGCCCTGTCAAAGCAAGAGATGGC
TAGTGCTTCATCCAGCCAAAGAGGTCGAAGTGGTTCTGGAAACTTTGGTGGTGGTCGTGGAGGTGGTTTCGGTGGGAATG
ACAACTTCGGTCGTGGAGGAAACTTCAGTGGTCGTGGTGGCTTTGGTGGCAGCCGTGGTGGTGGTGGATATGGTGGCAGT
GGGGATGGCTATAATGGATTTGGTAATGATGGAAGCAATTTTGGAGGTGGTGGAAGCTACAATGATTTTGGCAATTACAA
CAATCAGTCTTCAAATTTTGGACCCATGAAGGGAGGAAATTTTGAAGGCAGAAGCTCTGGCCCCCATGGCGGTGGAGGCC
AATACTTTGCAAAACCACGAAACCAAGGTGGCTATGGCGGTTCCAGCAGCAGCAGTAGCTATGGCAGTGGCAGAAGATTT

Alignment

ORF - retro_hsap_1638 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.81 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
          MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
Retrocopy MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA

Parental  AMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR
          AMNARPHKVDGRVVEPKRAVSREDSQRP.AHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR
Retrocopy AMNARPHKVDGRVVEPKRAVSREDSQRPDAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDR

Parental  GSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGF
          GSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGF
Retrocopy GSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGGF

Parental  GGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGN
          GGNDNFGRGGN....................DGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGN
Retrocopy GGNDNFGRGGNXXXXXXXXXXXXXXXXXXXXDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGGN

Parental  FGGRSSGPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF
          F.GRSSGP.GGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF
Retrocopy FEGRSSGPHGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF

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	0.78 RPM	775.80 RPM
bodymap2_adrenal	1.39 RPM	1006.81 RPM
bodymap2_brain	0.73 RPM	373.10 RPM
bodymap2_breast	0.45 RPM	438.74 RPM
bodymap2_colon	0.41 RPM	730.72 RPM
bodymap2_heart	0.11 RPM	200.75 RPM
bodymap2_kidney	0.76 RPM	336.99 RPM
bodymap2_liver	0.08 RPM	126.11 RPM
bodymap2_lung	0.14 RPM	423.66 RPM
bodymap2_lymph_node	0.11 RPM	358.27 RPM
bodymap2_ovary	2.00 RPM	1611.66 RPM
bodymap2_prostate	0.52 RPM	619.57 RPM
bodymap2_skeletal_muscle	0.93 RPM	321.98 RPM
bodymap2_testis	0.40 RPM	521.76 RPM
bodymap2_thyroid	0.53 RPM	609.76 RPM
bodymap2_white_blood_cells	0.53 RPM	596.21 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_1638 was not detected

EST

No EST(s) were mapped for retro_hsap_1638 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_52011	362 libraries	589 libraries	842 libraries	31 libraries	5 libraries

The graphical summary, for retro_hsap_1638 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_1638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_1638 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	1.67 RPM
CEU_NA11843	2.05 RPM
CEU_NA11930	3.59 RPM
CEU_NA12004	1.33 RPM
CEU_NA12400	2.07 RPM
CEU_NA12751	1.63 RPM
CEU_NA12760	3.05 RPM
CEU_NA12827	1.89 RPM
CEU_NA12872	2.50 RPM
CEU_NA12873	1.69 RPM
FIN_HG00183	2.61 RPM
FIN_HG00277	1.89 RPM
FIN_HG00315	2.15 RPM
FIN_HG00321	1.99 RPM
FIN_HG00328	2.20 RPM
FIN_HG00338	2.17 RPM
FIN_HG00349	3.39 RPM
FIN_HG00375	1.93 RPM
FIN_HG00377	2.27 RPM
FIN_HG00378	1.59 RPM
GBR_HG00099	2.56 RPM
GBR_HG00111	2.21 RPM
GBR_HG00114	1.63 RPM
GBR_HG00119	1.44 RPM
GBR_HG00131	1.38 RPM
GBR_HG00133	1.66 RPM
GBR_HG00134	1.53 RPM
GBR_HG00137	1.90 RPM
GBR_HG00142	1.69 RPM
GBR_HG00143	1.63 RPM
TSI_NA20512	1.58 RPM
TSI_NA20513	1.60 RPM
TSI_NA20518	4.33 RPM
TSI_NA20532	1.87 RPM
TSI_NA20538	2.03 RPM
TSI_NA20756	2.82 RPM
TSI_NA20765	1.55 RPM
TSI_NA20771	2.95 RPM
TSI_NA20786	1.65 RPM
TSI_NA20798	1.59 RPM
YRI_NA18870	2.98 RPM
YRI_NA18907	1.21 RPM
YRI_NA18916	1.60 RPM
YRI_NA19093	0.99 RPM
YRI_NA19099	1.76 RPM
YRI_NA19114	1.52 RPM
YRI_NA19118	1.53 RPM
YRI_NA19213	1.32 RPM
YRI_NA19214	1.01 RPM
YRI_NA19223	1.39 RPM

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Indel association:

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