RetrogeneDB ID: retro_btau_825

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:72106449..72107282(+)
• Located in intron of: ENSBTAG00000020855

Retrocopy information

• Ensembl ID: ENSBTAG00000048209
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TSG101
• Ensembl ID: ENSBTAG00000013563
• Aliases: None
• Description: tumor susceptibility gene 101 protein [Source:RefSeq peptide;Acc:NP_001091464]

Sequence

>retro_btau_825
AAGTACAAATACAGAGACCTAACTGTATGTGAAACTATTAACGTTATTACTTTATACAAAGATCTCAAACCTGTATTGGA
TTCATACGTTTTTAATGATGGTAGTTCCAGGGAACTAATGAACCTTACTGGAACAATTCCTGTGCCTTATAGAAGTAATA
CATAGAATATTCCAATCTGCCTGTGGCTGCTGGACACATATCCGTATAATCCCCCTATCTGTTTTGTTAAGCCTACTAGC
TCAATGACTATTAAAACAGGAAAGCATGTGGATGCTAATGGTAAGATACGTCTTCCTTATCTACATGAATGGAAGCACCC
ACAGTCAGACTTACTGGGGCTTATTCAAGTCATGATTGTGGTGTTTGGAGATGAACCTCCAGTCTTCTCTCGTCCTACTG
TTTCAGCATCCTATCCACCATACCAGGCAATAGGGCCACAAGATTCTTCCTACATGCCAGGTATGACAAGTGGGATTTCT
GCATACCATCCGGGTACCCTCCCAATCCGAGTGGTTACCCAGGCTGTCCTTACCGACCTGGTGGTCAGTATCCTGCCACA
ACAAATTCCTAGTACCCTTCCCAGCCTCCTGTGACCACTCTTGGTCCCAGTAGAGATGGCACAATCAGCAAGGACACTAT
CCAAGCCTCTCTCATCTCAGCAGTCAGTGACAGACTGAGATGGCGGATGAAGGAGGAAACGGATTGTGCCCAGGCAGAAC
TCAATGCCTTGAAACGAACAGAGGAAGACCTGAAAAAAGGTCACCAGAAACTCAAAGAGATGGTTACCCAAGAAGTAGCT
GAGGTTGATAAAAACATAGAACTTTTGAGAAAG

Alignment

ORF - retro_btau_825 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.43 %
• Parental protein coverage: 71.87 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KYKYRDLTVRETVNVISLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYN
          KYKYRDLTV.ET.NVI.LYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYR.NT.NIPICLWLLDTYPYN
Retrocopy KYKYRDLTVCETINVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRSNT*NIPICLWLLDTYPYN

Parental  PPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRPTVSASYPP
          PPICFVKPTSSMTIKTGKHVDANGKI.LPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRPTVSASYPP
Retrocopy PPICFVKPTSSMTIKTGKHVDANGKIRLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFSRPTVSASYPP

Parental  YQATGPPNTSYMPGMPSGISAY-PSGYPPNPSGYTGCPYPPGGQYPATTSSQYPSQPPVTTVGPSRDGTI
          YQA.GP...SYMPGM.SGISAY.PSGYPPNPSGY.GCPY.PGGQYPATT.S.YPSQPPVTT.GPSRDGTI
Retrocopy YQAIGPQDSSYMPGMTSGISAY<PSGYPPNPSGYPGCPYRPGGQYPATTNS*YPSQPPVTTLGPSRDGTI

Parental  SEDTIRASLISAVSDKLRWRMKEEMDRAQAELNALKRTEEDLKKGHQKLEEMVNRLDQEVAEVDKNIELL
          S.DTI.ASLISAVSD.LRWRMKEE.D.AQAELNALKRTEEDLKKGHQKL.EMV....QEVAEVDKNIELL
Retrocopy SKDTIQASLISAVSDRLRWRMKEETDCAQAELNALKRTEEDLKKGHQKLKEMVT---QEVAEVDKNIELL

Parental  RK
          RK
Retrocopy RK

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	3.32 RPM
ERP005899_muscle	0.00 RPM	21.33 RPM
SRP017611_brain	0.05 RPM	6.94 RPM
SRP017611_kidney	0.06 RPM	11.02 RPM
SRP017611_liver	0.00 RPM	4.38 RPM
SRP030211_testis	0.02 RPM	54.85 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_825 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_825 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_825 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013563	4 retrocopies	retro_btau_1009, retro_btau_698, retro_btau_825 , retro_btau_979,
Canis familiaris	ENSCAFG00000009279	1 retrocopy	retro_cfam_1615,
Cavia porcellus	ENSCPOG00000011994	1 retrocopy	retro_cpor_1420,
Myotis lucifugus	ENSMLUG00000016353	2 retrocopies	retro_mluc_1133, retro_mluc_1713,
Mus musculus	ENSMUSG00000014402	1 retrocopy	retro_mmus_1350,