RetrogeneDB ID: retro_btau_748

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 19:3972274..3973002(+)
• Located in intron of: ENSBTAG00000036115

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSBTAG00000036115
• Aliases: None
• Description: None

Sequence

>retro_btau_748
TTACAAACCTACTATAAATCAAATTCCAAACAGGCCATCCCCAACTTTTAGTAAGAATGCAAAGAAGACTTGGAATTAAT
AATGTGTCTCTAATATCTTCATTAGTTCAAGATAACAAGACGTATGTTAAAGCAAGGGTCAACAAAGATGATCATAACTC
TGACTTTCTTTGAGAAACGAGTGGAGAGAGTGCATTTTCAGCCTCCAGAACTTTAAATGTGCCATACATACCAAAGCCTC
ATAGCAGCCAGATATTTGCTAATACAAGCGCTGTAAGTCCATGTGACTTACCTTCCCCATCACCAATATCACTTAGACAA
ACAGACCAGATTGTAGTAGATCAACCTGCTGTTTTTAAAACACTGAGCATTTTTAATTGGCACTCACAAAGCAGCTACAC
TCAGGTAAATGGCCACGTTGAGGACTTCGCTACTACAACTACATCTACTTCTCAGAACCACATTGTGTCTCCATTACAAA
TCAGTTATTCCAGACTGATGGTGGAATCTTCTAAATTTCCAGTCACATATAGCAATATGTCAGCACATGACAGCCCTTTT
CCTATCCTGCAAGAGACAGGCAACTCATGGTCCTCAATGTCAATGATCGCTTATACATCTGCCTCCTCTCTTTCAAGTCA
ACTGATCAACAATCATCATCAGATGAAAACTATGCTAATTAAAACTGACCTATCAAATAAGTGTCAGATTATGGAGCCTA
AAGAAGAT

Alignment

ORF - retro_btau_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.34 %
• Parental protein coverage: 59.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQTYYKSNSKQ-GHPQLLVRMQRRLGINNVSLISSLVQDNKTYVKARVNKDDHNSDFLRETSGESAFSAS
          LQTYYKSNSKQ.GHPQLLVRMQRRLGINNVSLISSLVQDNKTYVKARVNKDDHNSDFL.ETSGESAFSAS
Retrocopy LQTYYKSNSKQ<GHPQLLVRMQRRLGINNVSLISSLVQDNKTYVKARVNKDDHNSDFL*ETSGESAFSAS

Parental  RTLNVPYIPKPHSSQIFDNTSAVSPCDLPSPSPISLRQTDQIVVDQPAVFKTLSIFNWHSHSSYTQVNGH
          RTLNVPYIPKPHSSQIF.NTSAVSPCDLPSPSPISLRQTDQIVVDQPAVFKTLSIFNWHS.SSYTQVNGH
Retrocopy RTLNVPYIPKPHSSQIFANTSAVSPCDLPSPSPISLRQTDQIVVDQPAVFKTLSIFNWHSQSSYTQVNGH

Parental  VEDFATTTTSTSQNHIVSPLQSSYSGLMVESSKFPVTYSNINMSAHDSPFPILQETGNSWSSMSMIAYTS
          VEDFATTTTSTSQNHIVSPLQ.SYS.LMVESSKFPVTYS..NMSAHDSPFPILQETGNSWSSMSMIAYTS
Retrocopy VEDFATTTTSTSQNHIVSPLQISYSRLMVESSKFPVTYS--NMSAHDSPFPILQETGNSWSSMSMIAYTS

Parental  ASSLSSQLINNHHQMKAMLIKTDLSNKCQIMEPKED
          ASSLSSQLINNHHQMK.MLIKTDLSNKCQIMEPKED
Retrocopy ASSLSSQLINNHHQMKTMLIKTDLSNKCQIMEPKED

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	0.00 RPM
ERP005899_muscle	0.00 RPM	0.00 RPM
SRP017611_brain	0.00 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 RPM
SRP030211_testis	0.04 RPM	0.08 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_748 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_748 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_748 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036115	3 retrocopies	retro_btau_549, retro_btau_681, retro_btau_748 ,