RetrogeneDB ID: retro_btau_1673

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:39819592..39820549(+)
• Located in intron of: ENSBTAG00000016584

Retrocopy information

• Ensembl ID: ENSBTAG00000007750
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPA1
• Ensembl ID: ENSBTAG00000001553
• Aliases: HNRNPA1, HNRPA1, hnRNP A1
• Description: Heterogeneous nuclear ribonucleoprotein A1 [Source:UniProtKB/Swiss-Prot;Acc:P09867]

Sequence

>retro_btau_1673
ATGTCTAAATCAGAGTCTCCCAAAGAACCTGAACAGCTGCGGAAGCTCTTCATCAGAGGATTGAGCTTTGAAACAACCGA
GAGTCTGAGGAGCCATTTTGAGCAATGGGGAACGCTCACAGACTGTGTGGTAATGAGGGATCCAAACACCGAGCGCTCCA
GAGGCTTCGGGTTTGACACATACACCACAGTGGAGGAGGTGGATGCGGCCATGAATGCAAGGCCACACAAGGTGGACGAA
GAGTTGCGGAACCAAAGAGGGCCGTCTCAAGAGAAGATTCTCACAGACCTGGTGCCCACTTAACTGTGAAAAAGATTTTT
GTTGGTGGCATTAAAGAAGACACTGAAGAACATCACCTGAGAGATTATTTTGAACAGTATGGGAAAATTGAAGTGATTGA
AATCATGACTGACCAAGGCAGTGGCAAAAAGAGAGGCTTTGCTTTCGTACTCTTTGATGACATTGACTCTGCAGACAAGA
TTGTCATTCAGAAATACCACACTGTGAATGGCCACAACTGTGAAGTGAGAAAAGCACTGTCTAACCAAGAGATGGCTAGT
GCTTCATTCAGCCAGAGAGGTCGAAGTGGTTCTGGAAACTTTGGTGGCGGTCGTGGAGGTGGTTTTGGTGGGAATGACAA
CTTTGTTCATGGAGGAAACTTCAGTGGTCGAGGTGGCCTTGGTGGCAGCCGTGGTGGTGGCGGATATGGTGGCAGAGGGG
ATGGATATAATGGATCTGGTAATGATGGAAGTAATTTTGGAGGTAGCAGAAGCTACAATGATTTTGGCAATTACAACAAT
CAATCTTCAAATTTTGGACCCATGAAAGGAGGAAACTTTGGAGACAGAAGCTCTCTCCACCTATGGTGGTGGAGGCCAAT
ACTTTGCCAAACCACGAAACCAAGGTGGCTATGGTGGCTCCAGCAGCAGCAGTAGCTATGGCAGTGGCGGAAGGTTT

Alignment

ORF - retro_btau_1673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDA
          MSKSESPKEPEQLRKLFI.GLSFETT.ESLRSHFEQWGTLTDCVVMRDPNT.RSRGFGF.TY.TVEEVDA
Retrocopy MSKSESPKEPEQLRKLFIRGLSFETT-ESLRSHFEQWGTLTDCVVMRDPNTERSRGFGFDTYTTVEEVDA

Parental  AMNARPHKVDG-RVVEPKRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD
          AMNARPHKVD..RV.EPKRAVSREDS.RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD
Retrocopy AMNARPHKVDE<RVAEPKRAVSREDSHRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD

Parental  RGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEVRKALSKQEMASASSSQRGRSGSGNFGGGRGGG
          .GSGKKRGFAFV.FDD.DS.DKIVIQKYHTVNGHNCEVRKALS.QEMASAS.SQRGRSGSGNFGGGRGGG
Retrocopy QGSGKKRGFAFVLFDDIDSADKIVIQKYHTVNGHNCEVRKALSNQEMASASFSQRGRSGSGNFGGGRGGG

Parental  FGGNDNFGRGGNFSGRGGFGGSRGGGGYGGSGDGYNGFGNDGSNFGGGGSYNDFGNYNNQSSNFGPMKGG
          FGGNDNF..GGNFSGRGG.GGSRGGGGYGG.GDGYNG.GNDGSNFGG..SYNDFGNYNNQSSNFGPMKGG
Retrocopy FGGNDNFVHGGNFSGRGGLGGSRGGGGYGGRGDGYNGSGNDGSNFGGSRSYNDFGNYNNQSSNFGPMKGG

Parental  NFGGRSS-GPYGGGGQYFAKPRNQGGYGGSSSSSSYGSGRRF
          NFG.RSS...YGGGGQYFAKPRNQGGYGGSSSSSSYGSG.RF
Retrocopy NFGDRSS>STYGGGGQYFAKPRNQGGYGGSSSSSSYGSGGRF

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
ERP005899_liver	0.00 RPM	64.89 RPM
ERP005899_muscle	0.21 RPM	523.83 RPM
SRP017611_brain	0.14 RPM	164.49 RPM
SRP017611_kidney	0.12 RPM	249.12 RPM
SRP017611_liver	0.00 RPM	85.48 RPM
SRP030211_testis	0.07 RPM	109.87 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1673 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1673 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1673 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 216 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,
Bos taurus	ENSBTAG00000005726	4 retrocopies	retro_btau_1330, retro_btau_1535, retro_btau_193, retro_btau_228,
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
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,
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,