RetrogeneDB ID: retro_btau_354

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:76992207..76994088(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000007807
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HSPA8
• Ensembl ID: ENSBTAG00000013162
• Aliases: HSPA8, HSPA10, Hsc70
• Description: Heat shock cognate 71 kDa protein [Source:UniProtKB/Swiss-Prot;Acc:P19120]

Sequence

>retro_btau_354
GCCCGCGGCCCGGCTATTGGCATCGACCTGGGCACCACCTACTCGTGCGTGGGGGTCTTCCAACATGGCAAAGTGGAGAT
CATCGCCAACGACCAGGGCAACCGTACCACCCCCAGCTACGTGGCCTTCACCGACACCGAGCGCCTCATCGGCGATGCAG
CCAAGAACCAGGTGGCCATGAACCCCACCAACACCATCTTCGACGCCAAGAGGCTGATTGGTCGGAAGTTCGAGGACGCC
ACAGTGCAGTCAGACATGAAACACTGGCCGTTCCGGGTGGTGAGCGAGGGAGGAAAGCCCAAAGTGCAGGTGGAGTACAA
AGGAGAGATCAAGACCTTCTTCCCCGAGGAGATCTCCTCCATGGTCCTCACTAAAATGAAGGAGATCGCCGAAGCCTACC
TGGGGGGCAAGGTGCAGAGCGCGGTCATCACCGTCCCGGCCTATTTCAATGACTCGCAGCGCCAGGCCACCAAGGACGCG
GGCACCATTACGGGCCTCAACGTGCTGCGCATCATCAACGAGCCCACGGCGGCGGCCATTGCCTACGGTCTGGACAAGAA
GGGCTGCGCGGGAGGCGAGAAGAACGTGCTCATTTTCGACCTGGGCGGCGGCACCTTCGACGTGTCCATCCTGACCATCG
AGGACGGCATCTTCGAGGTGAAGTCCACGGCTGGTGACACTCATCTGGGCGGGGAGGACTTCGATAACCGCATGGTGAGC
CACCTGGCGGAGGAGTTCAAACGCAAGCACAAGAAGGACATTGCACCCAACAAGCGCGCGGTGCGGCGACTCCGCACCGC
CTGCGAGCGCGCCAAGCGCACCCTGAGCTCGTCCACGCAGGCCAGCATCGAGATCGACTCGCTCTACGAGGGCGTGGATT
TCTACACTTCCATCACCCGCGCTCGCTTCGAGGAGCTCAACGCCGACCTTTTCCGCGGTACCCTGGAGCCGGTGGAGAAG
GCTCTGCGCGATGCCAAGCTGGACAAGGGCCAGATCCAGGAGATCGTGCTGGTGGGCGGCTCCACTCGCATCCCCAAGAT
CCAGAAGCTGCTGCAGGATTTCTTCAATGGCAAGGAGCTCAACAAGAGCATCAACCCCGACGAGGCGGTGGCCTACGGAG
CCGCGGTGCAGGCGGCCATTCTCATTGGGGACAAGTCAGAGAATGTACAGGACCTGCTGCTACTCGACGTGACCCCGTTG
TCCCTGGGCATCGAGACGGCTGGCGGCGTCATGACTCCGCTCATCAAAAGGAACACCACGATCCCCACCAAGCAGACGCA
GACCTTCACCACATACTCAGACAACCAGAGCAGCGTGCTGGTGCAGGTGTACGAGGGCGAACGGGCCATGACCAAGGACA
ATAACCTGTTGGGCAAGTTCGACCTGACCGGGATCCCCCCAGCGCCCCGCGGGGTCCCCCAGATCGAGGTCACCTTCGAC
ATCGACGCCAATGGCATCCTCAACGTCACCGCCGCCGACAAGAGCACCGGTAAAGAAAACAAAATCACCATTACCAACGA
CAAGGGTCGTCTGAGCAAGGATGACATTGACCGGATGGTGCAGGAGGCAGAGCGGTACAAGTCGGAAGATGAGGCCAATC
GCGACCGAGTAGCCGCCAAAAACGCTGTGGAGTCCTATACCTATAACATCAAGCAGACGGTGGAAGACGAGAAACTGAGG
GGCAAAATTAGCGATCAGGACAAAAACAAGATTCTCGACAAGTGTCAGGAGGTGATCAACTGGCTCGACCGGAACCAGAT
GGCGGAAAAAGATGAGTATGAACACAAGCAGAAAGAGCTCGAAAGAGTGTGCAACCCCATCATCAGCAAACTATACCAAG
GCGGCCCTGGCGGCGGCGGCGGTTCAGGAGCATCCGGGGGA

Alignment

ORF - retro_btau_354 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.8 %
• Parental protein coverage: 96.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAK
          ..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNT.FDAK
Retrocopy ARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAK

Parental  RLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTN
          RLIGR.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGE.K.F.PEE.SSMVLTKMKEIAEAYLG..V..
Retrocopy RLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGEIKTFFPEEISSMVLTKMKEIAEAYLGGKVQS

Parental  AVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKK--VGAERNVLIFDLGGGTFDVSI
          AV.TVPAYFNDSQRQATKDAGTI.GLNVLRIINEPTAAAIAYGLDKK...G.E.NVLIFDLGGGTFDVSI
Retrocopy AVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGCAGGEKNVLIFDLGGGTFDVSI

Parental  LTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQ
          LTIEDGIFEVKSTAGDTHLGGEDFDNRMV.H...EFKRKHKKDI..NKRAVRRLRTACERAKRTLSSSTQ
Retrocopy LTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIAPNKRAVRRLRTACERAKRTLSSSTQ

Parental  ASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKL
          ASIEIDSLYEG.DFYTSITRARFEELNADLFRGTL.PVEKALRDAKLDK.QI..IVLVGGSTRIPKIQKL
Retrocopy ASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQKL

Parental  LQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTT
          LQDFFNGKELNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLLLDVTPLSLGIETAGGVMT.LIKRNTT
Retrocopy LQDFFNGKELNKSINPDEAVAYGAAVQAAILIGDKSENVQDLLLLDVTPLSLGIETAGGVMTPLIKRNTT

Parental  IPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
          IPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTGIPPAPRGVPQIEVTFDIDANGILNV.
Retrocopy IPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTGIPPAPRGVPQIEVTFDIDANGILNVT

Parental  AVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQ
          A.DKSTGKENKITITNDKGRLSK.DI.RMVQEAE.YK.EDE..RD.V..KN..ESY..N.K.TVEDEKL.
Retrocopy AADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANRDRVAAKNAVESYTYNIKQTVEDEKLR

Parental  GKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGMPGG
          GKI.D.DK.KILDKC.E.INWLD.NQ.AEK.E.EH.QKELE.VCNPII.KLYQ..GG..GG...G..GG
Retrocopy GKISDQDKNKILDKCQEVINWLDRNQMAEKDEYEHKQKELERVCNPIISKLYQ--GGPGGGGGSGASGG

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	0.79 RPM	567.68 RPM
ERP005899_muscle	19.58 RPM	1534.63 RPM
SRP017611_brain	19.46 RPM	1548.12 RPM
SRP017611_kidney	50.97 RPM	1140.51 RPM
SRP017611_liver	1.66 RPM	546.53 RPM
SRP030211_testis	327.69 RPM	313.37 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

19 EST(s) were mapped to retro_btau_354 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG689054	76992112	76992620	99.5	505	3	502
BG938089	76993421	76993658	100	237	0	237
CB220729	76993202	76993541	100	339	0	339
CK963436	76992117	76992761	100	644	0	644
DT829281	76992087	76992926	99.9	837	1	836
DT836831	76992087	76992908	99.9	820	1	819
DT851627	76992089	76992920	99.7	827	3	824
DV925765	76992132	76992760	100	628	0	628
DY090917	76993294	76993659	99.5	363	2	361
DY158247	76993294	76993632	98	331	7	324
DY184697	76992379	76992621	99.6	241	1	240
DY187454	76992327	76992617	100	290	0	290
EE252405	76992087	76992907	100	820	0	820
EE335561	76992082	76992910	100	828	0	828
EE360663	76992124	76992948	99.9	823	1	822
EE382115	76992095	76992898	99.8	801	2	799
EH372937	76992087	76992848	99.8	759	2	757
EV609864	76992087	76992750	100	663	0	663
EV793034	76992087	76992900	100	813	0	813

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_354 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_68
Gorilla gorilla	retro_ggor_1053
Pongo abelii	retro_pabe_183
Canis familiaris	retro_cfam_140

---

Parental genes homology:

Parental genes homology involve 32 parental genes, and 108 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca	ENSAMEG00000008425	1 retrocopy	retro_amel_126,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Bos taurus	ENSBTAG00000013162	1 retrocopy	retro_btau_354 ,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
Callithrix jacchus	ENSCJAG00000007648	5 retrocopies	retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Dipodomys ordii	ENSDORG00000015467	1 retrocopy	retro_dord_16,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Felis catus	ENSFCAG00000001132	6 retrocopies	retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens	ENSG00000109971	8 retrocopies	retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Gorilla gorilla	ENSGGOG00000008381	8 retrocopies	retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta	ENSMMUG00000004696	7 retrocopies	retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus	ENSMUSG00000015656	8 retrocopies	retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Oryctolagus cuniculus	ENSOCUG00000015533	4 retrocopies	retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pongo abelii	ENSPPYG00000003987	9 retrocopies	retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Pan troglodytes	ENSPTRG00000004404	5 retrocopies	retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Tursiops truncatus	ENSTTRG00000011139	6 retrocopies	retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,