RetrogeneDB ID: retro_btau_1507

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 6:99834206..99835376(-)
• Located in intron of: ENSBTAG00000005744

Retrocopy information

• Ensembl ID: ENSBTAG00000046700
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBPJ
• Ensembl ID: ENSBTAG00000003602
• Aliases: None
• Description: Recombining binding protein suppressor of hairless [Source:UniProtKB/Swiss-Prot;Acc:Q3SZ41]

Sequence

>retro_btau_1507
ATGGCGCCTGTTGTGACAGGAAAATTTGGTGAGCGGCTTCCACCTAAACAACTCACTAGGGAAGCTATGTGAAATTATTT
AAAAGAACGAGGGGATCAAACAGTGCTTATTCTTCATGCAAAAGTTGCACAGAAGTCATATGGAAATGAAAAAAGGTTTT
TTTGCCCTCCTTCTTGTGTGTATCTTATGGGCAGTGGATGGAACAAAAAAAAAAGAACAAATGGAACGCGATGGTTGTTC
AGAACAGGAATCTCAACCATGTGCTTTTATTGGAATAGGAAATAGTGACCAAGAAATGCAGCAACTGAACTTGGAAGAAA
AGAACTATTGCACAGCCAAAACATTGTATATATCTGATTCAGACAAGAGAAAGCACTTCATGCTGTCTGTAAAGATGTTC
TATGGCAACAGTGATGACATTGGTGTGTTCCTAAGCAAGCGGATAAAAGTCATCTCCAAACCTTCCAAAAAGAAGCCATC
ACTGAAAAATGCTGACCTCTGCATTGCCTCAGGAATAAAAGTGGCTCTGTTTAATAGACTCCGATCCCAGACAGTTAGCA
CCAGATACTTGCATGTAGAAGGTGGTAATTTCCATGCCAGTTTTCAGCAGTGGGGAGCATTTTACATTCATCTCTTGGAT
GATGATGAATCAGAAGGAGAAGAATTCACAGTCCGCGATGGATACATCCATTATGGACAAACAGTCAAACTTGTGTGTTC
AGTTACTGGCATGGCACTCCCAAGATTGATAATTAGGAAGGTTGATAAGCAGACCGCGTTACTGGATGCCGATGATCCTG
TGTCACAGCTCCACAAATGTGCGTTTTACCTTAAGGATACAGAAAGAATGTACTTGTGCCTTTCTCAAGAAAGAATAATC
CAGTTTCAGGCCACTCCATGCCCAAAAGAACGAAATAAAGAGATGATAAATGATGGAGCTTCCTGGACAATCATTAGTAC
AGATAAGGCAGAGTATACATTTTATGAGGGGGTGGGCCCTGTCCTTGCCCCAGTCACACCTGAGCCTGTCGTAGAAAGTC
TTCAGTTGAATGGCAGTGGGGACTAGCAATGCTTGAACTTACAGGACAGAGTTTCACTCCAAATTTACGAGTGTGGTTTG
GGGATGTAGAAGCTGAAACTATGTTGATGTGGAGAGAGTATGCTCTGTGT

Alignment

ORF - retro_btau_1507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.37 %
• Parental protein coverage: 80.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPVVTGKFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPPCVYLMGSGWKKK
          MAPVVTGKFGER.PPK.LTREAM.NYLKERGDQTVLILHAKVAQKSYGNEKRFFCPP.CVYLMGSGW...
Retrocopy MAPVVTGKFGERLPPKQLTREAM*NYLKERGDQTVLILHAKVAQKSYGNEKRFFCPPSCVYLMGSGWNXX

Parental  K-EQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDD
          ..EQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLE.KNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDD
Retrocopy X>EQMERDGCSEQESQPCAFIGIGNSDQEMQQLNLEEKNYCTAKTLYISDSDKRKHFMLSVKMFYGNSDD

Parental  IGVFLSKRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQWGAFYI
          IGVFLSKRIKVISKPSKKK.SLKNADLCIASG.KVALFNRLRSQTVSTRYLHVEGGNFHAS.QQWGAFYI
Retrocopy IGVFLSKRIKVISKPSKKKPSLKNADLCIASGIKVALFNRLRSQTVSTRYLHVEGGNFHASFQQWGAFYI

Parental  HLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKD
          HLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKD
Retrocopy HLLDDDESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKD

Parental  TERMYLCLSQERIIQFQATPCPKEPNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQL
          TERMYLCLSQERIIQFQATPCPKE.NKEMINDGASWTIISTDKAEYTFYEG.GPVLAPVTP.PVVESLQL
Retrocopy TERMYLCLSQERIIQFQATPCPKERNKEMINDGASWTIISTDKAEYTFYEGVGPVLAPVTPEPVVESLQL

Parental  NGGGD-VAMLELTGQNFTPNLRVWFGDVEAETMYRCGESMLC
          NG.GD..AMLELTGQ.FTPNLRVWFGDVEAETM....E..LC
Retrocopy NGSGD<LAMLELTGQSFTPNLRVWFGDVEAETMLMWREYALC

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	3.24 RPM
ERP005899_muscle	0.11 RPM	13.41 RPM
SRP017611_brain	0.14 RPM	13.89 RPM
SRP017611_kidney	0.18 RPM	16.36 RPM
SRP017611_liver	0.00 RPM	5.81 RPM
SRP030211_testis	0.07 RPM	10.21 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1507 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1507 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003602	1 retrocopy	retro_btau_1507 ,
Choloepus hoffmanni	ENSCHOG00000001582	4 retrocopies	retro_chof_1172, retro_chof_1278, retro_chof_2449, retro_chof_371,
Homo sapiens	ENSG00000168214	6 retrocopies	retro_hsap_4169, retro_hsap_4171, retro_hsap_4173, retro_hsap_4174, retro_hsap_4256, retro_hsap_4316,
Gorilla gorilla	ENSGGOG00000004582	1 retrocopy	retro_ggor_2853,
Mus musculus	ENSMUSG00000039191	2 retrocopies	retro_mmus_2348, retro_mmus_2819,
Nomascus leucogenys	ENSNLEG00000016895	1 retrocopy	retro_nleu_2305,
Oryctolagus cuniculus	ENSOCUG00000013449	1 retrocopy	retro_ocun_1445,
Pan troglodytes	ENSPTRG00000015968	1 retrocopy	retro_ptro_2829,
Tursiops truncatus	ENSTTRG00000009022	2 retrocopies	retro_ttru_1151, retro_ttru_1593,