RetrogeneDB ID: retro_btau_979

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 22:51686543..51687716(+)
• Located in intron of: ENSBTAG00000014205

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

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_979
ATGGCGGGGTCGGAGAGCCAGCTCAAGAAAATGGTGTCCAAGTACAAATACAAAGACCTAACTGTACGTGAAACTGTTAA
CGTTATTAGTTTATACAAAGATCTCAAACCTGTATTGGACTCATATGTTTTTAATGATGGCAGTTCCAGGGAACTAATGA
ACCTTACTGGAACAATTCCTGTGCCTTATAGAGGTAATACATACAATATTCCAATCTGCCTGTGGCTGCTGGACACATAT
CCGTATAATCCCCCTATCTGTTTCGTTAAGCCTACTAGCTCAATGACTATTAAAACAGGAAAGCATGTGGATGCTAATGG
GAAGATATATCTTCCTTATCTACATGAATGGAAGCACCCACAGTCAGACTTGTTGGGGCTTATTCAAGTCATGATTGTGG
TGTTTGGAGATGAACCTCCGGTCTTCTCTCGTCCTACTGTTTCAGCATCCTATCCACCATACCAGGCAACAGGGCCACCA
AATACTTCCTACATGCCAGGCATGCCAAGTGGGATTTCTGCATACCCATCCGGGTACCCTCCCAATCCCAGTGGTTACAC
AGGCTGTCCTTACCCACCTGGTGGTCAGTATCCTGCCACAACAAGTTCCCAGTACCCTTCCCAGCCTCCTGTGACCACTG
TTGGTCCCAGTAGAGATGGCACAATCAGTGAGGACACTATCCGAGCCTCTCTCATCTCAGCGGTCAGCGACAAACTGAAA
TGGCGGGTGAAGGAGGAGATGGATCGTGCCCAGGCAGAACTCAACGCCTTGAAACGAACAGAGGAAGACCTGAAAAAAGG
TCACCAGAAACTCGAGGAGATGGTTAACCGTTTAGATCAAGAAGTAGCTGAGGTTGATAAAAACATAGAACTTTTGAGAA
AGAAGGATGAAGAACTCAGTTCTGCTCTGGAGAAAATGGAAAATCAGTCTGAAAACAATGATATTGATGAAGTTATCATT
CCCACAGCCCCACTATACAAACAGATCCTAAATCTGTATGCAGAGGAAAATGCTATTGAAGACACTATTTTTTACCTGGG
AGAAGCCTTGAGGCGGGGAGTCATAGACTTAGATGTCTTCCTAAAGCATGTACGTCTTCTGTCCCGTAAACAGTTCCAGC
TGAGGGCACTAATGCAGAAAGCAAGAAAGACTGCCGGTCTCAGTGACCTCTAC

Alignment

ORF - retro_btau_979 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.23 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGSESQLKKMVSKYKYRDLTVRETVNVISLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNI
          MAGSESQLKKMVSKYKY.DLTVRETVNVISLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNI
Retrocopy MAGSESQLKKMVSKYKYKDLTVRETVNVISLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNI

Parental  PICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPP
          PICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPP
Retrocopy PICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPP

Parental  VFSRPTVSASYPPYQATGPPNTSYMPGMPSGISAYPSGYPPNPSGYTGCPYPPGGQYPATTSSQYPSQPP
          VFSRPTVSASYPPYQATGPPNTSYMPGMPSGISAYPSGYPPNPSGYTGCPYPPGGQYPATTSSQYPSQPP
Retrocopy VFSRPTVSASYPPYQATGPPNTSYMPGMPSGISAYPSGYPPNPSGYTGCPYPPGGQYPATTSSQYPSQPP

Parental  VTTVGPSRDGTISEDTIRASLISAVSDKLRWRMKEEMDRAQAELNALKRTEEDLKKGHQKLEEMVNRLDQ
          VTTVGPSRDGTISEDTIRASLISAVSDKL.WR.KEEMDRAQAELNALKRTEEDLKKGHQKLEEMVNRLDQ
Retrocopy VTTVGPSRDGTISEDTIRASLISAVSDKLKWRVKEEMDRAQAELNALKRTEEDLKKGHQKLEEMVNRLDQ

Parental  EVAEVDKNIELLRKKDEELSSALEKMENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDTIFYLGEAL
          EVAEVDKNIELLRKKDEELSSALEKMENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDTIFYLGEAL
Retrocopy EVAEVDKNIELLRKKDEELSSALEKMENQSENNDIDEVIIPTAPLYKQILNLYAEENAIEDTIFYLGEAL

Parental  RRGVIDLDVFLKHVRLLSRKQFQLRALMQKARKTAGLSDLY
          RRGVIDLDVFLKHVRLLSRKQFQLRALMQKARKTAGLSDLY
Retrocopy RRGVIDLDVFLKHVRLLSRKQFQLRALMQKARKTAGLSDLY

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	0.16 RPM	21.33 RPM
SRP017611_brain	0.32 RPM	6.94 RPM
SRP017611_kidney	0.06 RPM	11.02 RPM
SRP017611_liver	0.08 RPM	4.38 RPM
SRP030211_testis	1.67 RPM	54.85 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_btau_979 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
CA036004	51686819	51686959	98.6	138	2	136

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_979 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_979 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,