RetrogeneDB ID: retro_btau_698

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 18:45161779..45162951(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000018080
• 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_698
ATGGTGAAGTCAGAGAGCCAGCTCAAGAAAATGGTGTCCAAGTACAAATACAGAGACCTAACTGTACGTGAAACTGTTAA
CGTTATTACTCTATACAAAGATTTCAGACCTGTATTGGATTCATATGTTTTTAATGATGGCAGTTCCAGGGAACTAATGA
ACCTTACTGGAACAATTTCTGTGGGTTATAGAGGTCATACATACAATATTTCAATCTGCCTGTGGCTGTTGGACACATAT
CCATATAATCCCCCTATCTGTTTCGTTAAGCCTACTAGCTCAATGACTATTAAAATAGGAAAGCACGTGGATGCTAATGG
GAAGATATATTTTCCTAATCTACATGAATGGGAGCACCCCAGTCAGACTTGTTGGGGCTTATTCAAGTCATGATTGTGGT
GTTTGGAGATGAACCTCCAGTCTTCTCTCATCCTATTGTTTCAGCATCCTATCCACCATATCAGGCAACAGGGCAACCAA
ATAATTCCTACATGCCAGGCATGCCAAGTAGGATTTCTGCATACCCATCTGGGTACCCTCCCAATCCCAGTGGTTACACA
GGCTGTCCTTACCCACCTGGTGGTCAGTATCCTGCCACAACAAGTTCCCAGTACCCTTCCCAGCCTCCTGTGACCGCTGT
TGGTCCCAGTAGGGGTGGCACAGTCAGCAAGGACACTATCCGAGCCTCTCTCATCTCAGCGGTCAGTGACAAACTGAGAT
GTCGGATGAAGGAGGAAATGGATTGTGCCCAGGCAGAACTCAATGCCTTGAAACGAACAGAGGAAGACCTGAAAAAAGGT
CACCAGAAACTCGAAGAGATGGTTAACCATTAAGATCAAGAAGTAGCTGAGGTTGATAAAAACATAGAACTTTTGAGAAA
GAAGGATGAAGAACTCAGTTCTGCTCTGGAGAAAATGGAAAATCAATCTGAAAACAATGATATTGATGAAGTTATCATTC
CCACAGCCCCACTATACAAACAGATCCTAAATCTGTATGCAGAGGAAAATGCTATTGAAGACACTGTTTTTTACCTGGGA
GAAGCCTTGAGGCAGGGAGTAATAGATCTAGATGTCTTCCTAAAGCATGTACATCTTCTGTCCCATAATCAGTTCCAGCT
GAGGGTACTAATGCAGAAAGCAAGAAAGACTGCTGGTCTCAGTGACTTCTAC

Alignment

ORF - retro_btau_698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGSESQLKKMVSKYKYRDLTVRETVNVISLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNI
          M..SESQLKKMVSKYKYRDLTVRETVNVI.LYKD..PVLDSYVFNDGSSRELMNLTGTI.V.YRG.TYNI
Retrocopy MVKSESQLKKMVSKYKYRDLTVRETVNVITLYKDFRPVLDSYVFNDGSSRELMNLTGTISVGYRGHTYNI

Parental  PICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHP-QSDLLGLIQVMIVVFGDEP
          .ICLWLLDTYPYNPPICFVKPTSSMTIK.GKHVDANGKIY.P.LHEW.HP.QSDLLGLIQVMIVVFGDEP
Retrocopy SICLWLLDTYPYNPPICFVKPTSSMTIKIGKHVDANGKIYFPNLHEWEHP<QSDLLGLIQVMIVVFGDEP

Parental  PVFSRPTVSASYPPYQATGPPNTSYMPGMPSGISAYPSGYPPNPSGYTGCPYPPGGQYPATTSSQYPSQP
          PVFS.P.VSASYPPYQATG.PN.SYMPGMPS.ISAYPSGYPPNPSGYTGCPYPPGGQYPATTSSQYPSQP
Retrocopy PVFSHPIVSASYPPYQATGQPNNSYMPGMPSRISAYPSGYPPNPSGYTGCPYPPGGQYPATTSSQYPSQP

Parental  PVTTVGPSRDGTISEDTIRASLISAVSDKLRWRMKEEMDRAQAELNALKRTEEDLKKGHQKLEEMVNRLD
          PVT.VGPSR.GT.S.DTIRASLISAVSDKLR.RMKEEMD.AQAELNALKRTEEDLKKGHQKLEEMVN..D
Retrocopy PVTAVGPSRGGTVSKDTIRASLISAVSDKLRCRMKEEMDCAQAELNALKRTEEDLKKGHQKLEEMVNH*D

Parental  QEVAEVDKNIELLRKKDEELSSALEKMENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDTIFYLGEA
          QEVAEVDKNIELLRKKDEELSSALEKMENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDT.FYLGEA
Retrocopy QEVAEVDKNIELLRKKDEELSSALEKMENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDTVFYLGEA

Parental  LRRGVIDLDVFLKHVRLLSRKQFQLRALMQKARKTAGLSDLY
          LR.GVIDLDVFLKHV.LLS..QFQLR.LMQKARKTAGLSD.Y
Retrocopy LRQGVIDLDVFLKHVHLLSHNQFQLRVLMQKARKTAGLSDFY

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	3.32 RPM
ERP005899_muscle	0.00 RPM	21.33 RPM
SRP017611_brain	0.00 RPM	6.94 RPM
SRP017611_kidney	0.00 RPM	11.02 RPM
SRP017611_liver	0.00 RPM	4.38 RPM
SRP030211_testis	0.01 RPM	54.85 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_698 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_698 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_698 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,