RetrogeneDB ID: retro_btau_1721

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: GJ058447.1:26609..27223(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSPY-M2
• Ensembl ID: ENSBTAG00000031517
• Aliases: TSPY, TSPY-M1, TSPY1
• Description: testis-specific Y-encoded protein 1 [Source:RefSeq peptide;Acc:NP_001231537]

Sequence

>retro_btau_1721
GTTGTAATGCCAGGCAAAGAGACCACCCTCTTCAGGTTGGAGGCAGTGGACGACAGTGAGCCCCTGGTGGACGGAGATGC
GGCAGGGATCGGGCGGGGGTTCCAGCTGCCTGCAGAAGACATCATGGAGGAGGTGGAGGTTGTGGCAGATGAAGAGCAGC
AATAGGGGTCCTCCCAGGAGCTGAAGAGAAGATGATGGAGGAGCAGGGCCAGGAAAGGCCCAGGAGATCAACTGAGCTTC
TGGGGCAAGATGCACTGCAGGAACTGGCCGCCATGAAGGTGGAACTGAGGTCTGAGCATGAGAAAAACTGCAGGGCCTAC
TTTCAGTTCATGCGCAAGAACCATCAGAGGAGGAAGCCTGACTTGGCTCGGAGGAGTGCCATCATCCAGGGCATCCCTTG
CTTGTGGGCCATAGCTTTATCCTTTCTGCTGCCCTTGGAGTCCGCTGCTCAGGAGGAGGAGGAGGTGCAGAAAACTTTTC
CCTCCTCCCTACCCTGGCAGGTGCAGTTGCAGAGCCATCCATGTTCCCCCTGCAAGGTGATCTTCTCCATTCAGGACCAA
CCCTACTTCTTGAGCACAGTGATCACTAAGTATAGTTACCTTGACATCGTTGGT

Alignment

ORF - retro_btau_1721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 64.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVTPGQEATLFRVEAVEEGEALVDGDVAGIGREFQLLAEDIVEEVEVVADEEQEQRPSQEL-EEKTVEEQ
          VV.PG.E.TLFR.EAV...E.LVDGD.AGIGR.FQL.AEDI.EEVEVVADEEQ....SQEL.EEK..EEQ
Retrocopy VVMPGKETTLFRLEAVDDSEPLVDGDAAGIGRGFQLPAEDIMEEVEVVADEEQQ*GSSQEL<EEKMMEEQ

Parental  GQERPGGPCERQELDALQALAALQVELSSEREQNRRAYVQFMRKNHQRRKRHLARRSAIIQGIPGFWAKA
          GQERP....E....DALQ.LAA..VEL.SE.E.N.RAY.QFMRKNHQRRK..LARRSAIIQGIP..WA.A
Retrocopy GQERPRRSTELLGQDALQELAAMKVELRSEHEKNCRAYFQFMRKNHQRRKPDLARRSAIIQGIPCLWAIA

Parental  IMSHPQVSVLISDQDQDFLGYMMDLKVQVR--SHPPSRCKLVFSFRDNPYFLNSVIIKEYYLDITG
          ........................L..QV...SHP.S.CK..FS..D.PYFL..VI.K..YLDI.G
Retrocopy LSFLLPLESAAQEEEEVQKTFPSSLPWQVQLQSHPCSPCKVIFSIQDQPYFLSTVITKYSYLDIVG

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	0.08 RPM	0.00 RPM
SRP030211_testis	0.07 RPM	0.74 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1721 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1721 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1721 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Bos taurus	ENSBTAG00000031517	2 retrocopies	retro_btau_1721 , retro_btau_667,