RetrogeneDB ID: retro_btau_877

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:84413664..84414878(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000009976
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAD23B
• Ensembl ID: ENSBTAG00000001926
• Aliases: None
• Description: UV excision repair protein RAD23 homolog B [Source:UniProtKB/Swiss-Prot;Acc:Q29RK4]

Sequence

>retro_btau_877
ATGCTGGTCACCCTGAAGACCCTCCAGCAGCAGACCTTCAAGATCGACATCGACCCCGATGAGACGGTGAGAGCACTGAA
AGAGAAGATTGAATCCGAAAAGGGTAAAGATGCCTTTCCTGTAGCAGGTCAAAAGTTAATTTATGCAGGCAAAATCCTCA
ATGATGATACTGCTCTAAAAGAATATAAAATTGATGAGAAAAACTTCATGGTGGTTATGGTGACAAAACCTAAAGCAGTG
ACAACACCAGCATCAGCTACAACTCAGCAAATTCTGCCGCCACCACCACAGTTAGTTCCTCCACAGTGCCAGCTGTGACT
CAGGCCCCAGCCCCTGCCCCCACTTCGGCTCCCACTTCCACACCTGCGTCTGTCACTCCAGCACCGACGACAGCATCTTC
TGAGCCTGCACCTGCTAGTGCAGCGAAGCAGGAGAAGCCTGCAGAGAGGCCAGTGGAAACCCCAGTGGCCACCACCCCAA
CGTCAACCGACAGTACATCAGGTGATTCTTCTCGGTCAAACCTTTTTGAAGATGCAACAAGTGCACTTGTGACAGGTCAG
TCTTACGAGAATATGGTAACTGAGATCATGTCAATGGGCGATGAACGAGAGCAAGTAATTGCAGCCCTGAGAGCCAGTTT
CAACAACCCTGACAGAGCAGTGGTGTATCTCTTAATGTGAATTCCTGGAGATTGAGAAAGTCAGGCTGTGGTTGACCCCC
CTCCAGCAGCTAGTACTGGGGCTCCTCAGTCTTCAGTGGCTGCAGCCGCAGCAACTACGACAGCAACAACTACAACAAGT
TCTGGAGGACACCCTCTTGAATTTTTACGGAATCAGCCTCAGTTTCAACAGATGAGGCAAATTATTCAACAGAATCCTTC
CCTGCTTCCAGCATTGCTACAACAGATAGGTCGAGAAAATCCTCAGTTACTTCAGCAAATTAGCCAACATCAGGAGCACT
TTATTCAGATGTTAAATGAACCAGTTCAAGAAGCTGGTGGTCAAGGAGGAGGGGGAGGAGGTGGCAGTGGAGGAATCGCA
GAAGCTGGAAGTGGTCATATGAACTACATTCAAGTAACGCCTCAGGAAAAAGAAGCTATAGAAAGGTTAAAGGCATCAGG
ATTTCCTGAAGGACTTGTGATACATGCATATTTTGCTTGTGAGAAGGAGAACTTGGCTGCCAATTTTCTTCTACAGCAAA
ACTTTGATGAAGAT

Alignment

ORF - retro_btau_877 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLVTLKTLQQQTFKIDIDPDETVRALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFV
          MLVTLKTLQQQTFKIDIDPDETVRALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNF.
Retrocopy MLVTLKTLQQQTFKIDIDPDETVRALKEKIESEKGKDAFPVAGQKLIYAGKILNDDTALKEYKIDEKNFM

Parental  VVMVTKPKAVTTPAPATTQQ-SNSAATTTVSSSTAPAVTQAPAPAPASAPTPTPVSVTPAPTTASSEPAP
          VVMVTKPKAVTTPA.A.T.Q..NSAATTTVSSST.PAVTQAPAPAP.SAPT.TP.SVTPAPTTASSEPAP
Retrocopy VVMVTKPKAVTTPASA-TTQ<ANSAATTTVSSSTVPAVTQAPAPAPTSAPTSTPASVTPAPTTASSEPAP

Parental  ASAAKQEKPAERPVETPVATTPTSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGYEREQVIA
          ASAAKQEKPAERPVETPVATTPTSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMG.EREQVIA
Retrocopy ASAAKQEKPAERPVETPVATTPTSTDSTSGDSSRSNLFEDATSALVTGQSYENMVTEIMSMGDEREQVIA

Parental  ALRASFNNPDRAVEYLLMGIPGDRESQAVVDPPPAASTGAPQSSVAAAAATTTATTTTTSSGGHPLEFLR
          ALRASFNNPDRAV.YLLM.IPGD.ESQAVVDPPPAASTGAPQSSVAAAAATTTA.TTTTSSGGHPLEFLR
Retrocopy ALRASFNNPDRAVVYLLM*IPGD*ESQAVVDPPPAASTGAPQSSVAAAAATTTA-TTTTSSGGHPLEFLR

Parental  NQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGSGGIA
          NQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGSGGIA
Retrocopy NQPQFQQMRQIIQQNPSLLPALLQQIGRENPQLLQQISQHQEHFIQMLNEPVQEAGGQGGGGGGGSGGIA

Parental  EAGGGHMNYIQVTPQEKEAIERLKALGFPEGLVIQAYFACEKNENLAANFLLQQNFDED
          EAG.GHMNYIQVTPQEKEAIERLKA.GFPEGLVI.AYFACEK.ENLAANFLLQQNFDED
Retrocopy EAGSGHMNYIQVTPQEKEAIERLKASGFPEGLVIHAYFACEK-ENLAANFLLQQNFDED

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	0.07 RPM	123.86 RPM
ERP005899_muscle	0.21 RPM	95.23 RPM
SRP017611_brain	1.78 RPM	66.01 RPM
SRP017611_kidney	0.77 RPM	65.14 RPM
SRP017611_liver	2.34 RPM	82.30 RPM
SRP030211_testis	0.11 RPM	39.78 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_877 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_877 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_877 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001926	1 retrocopy	retro_btau_877 ,
Callithrix jacchus	ENSCJAG00000016908	2 retrocopies	retro_cjac_3865, retro_cjac_4184,
Dasypus novemcinctus	ENSDNOG00000001174	2 retrocopies	retro_dnov_1982, retro_dnov_989,
Equus caballus	ENSECAG00000021928	1 retrocopy	retro_ecab_361,
Homo sapiens	ENSG00000119318	2 retrocopies	retro_hsap_2611, retro_hsap_3754,
Gorilla gorilla	ENSGGOG00000002511	1 retrocopy	retro_ggor_1829,
Loxodonta africana	ENSLAFG00000007533	1 retrocopy	retro_lafr_1109,
Macaca mulatta	ENSMMUG00000014944	2 retrocopies	retro_mmul_1476, retro_mmul_1725,
Nomascus leucogenys	ENSNLEG00000017319	1 retrocopy	retro_nleu_1590,
Oryctolagus cuniculus	ENSOCUG00000007316	1 retrocopy	retro_ocun_1429,
Otolemur garnettii	ENSOGAG00000014216	1 retrocopy	retro_ogar_3040,
Pongo abelii	ENSPPYG00000019477	2 retrocopies	retro_pabe_2344, retro_pabe_3162,
Pan troglodytes	ENSPTRG00000021229	1 retrocopy	retro_ptro_1760,
Sarcophilus harrisii	ENSSHAG00000011925	1 retrocopy	retro_shar_248,
Sus scrofa	ENSSSCG00000005436	1 retrocopy	retro_sscr_770,
Tursiops truncatus	ENSTTRG00000007597	1 retrocopy	retro_ttru_1401,