RetrogeneDB ID: retro_btau_1023

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 23:27835638..27836363(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRAGC
• Ensembl ID: ENSBTAG00000009368
• Aliases: None
• Description: ras-related GTP-binding protein C [Source:RefSeq peptide;Acc:NP_001069924]

Sequence

>retro_btau_1023
AACTTTACCATTTCTAAAGCCTACAAAGTTAACATAGACATGAATTTTGAGGTTTTTATTCACAAAGTTGATGGTCTGTC
TGATGATTACAAAATATAAACACAGAGGGACATTCATCAATGGGCCAATGATGACCTTGCAGATGCTGGGCTAGAAAAAC
TCCATCTTAGCTTTTATTTTACTAGTATTTATGACCATTCAACATTTGCAGCCTTTAGTAAGGTGCTGCAGAAACTATCC
CACAGCTACTGGCCTTGGAATACCTATTAAATACCTTTATATCAAATTCAGGTATTGAAAAAGCTTTTCTCTTTGATGTT
GTCAGCAAAATCTACATTACAACAGATAGTTCTCCTGTAGATATGCAGTCACAGGAACTTTGCTGTGACATGATTGATAT
TGTAATTGATGTGTGTTGTATGTTTGGGTTAAAGGAAAATAGAAGTGGAAGTGCTTACCACAAAGAGTCCAAGGCCATCA
TCAAGCTGAATAACACAACTGTCCTGTATTTAAAGGAGGTAACTAAATTTTTGGCACTGGTTTGCATCCATAGGGAAGAA
AGTTTTGAATGAAAAAGTTTAATAGACTATAACTTCCATTGTTTCCGAAAAGCTATTCATGAGGTTTTTGAGGTGGGTGT
GACTTCTCACAGAAGCTGTGGTCACCAGACCAGTGTCCCCAACCTGAAAGCTTTGACACGCAATTGCACACCATGAAACG
TCATC

Alignment

ORF - retro_btau_1023 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.19 %
• Parental protein coverage: 60.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HITVSKAYKVNPDMNFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFE
          ..T.SKAYKVN.DMNFEVFIHKVDGLSDD.KI.TQRDIHQ.ANDDLADAGLEKLHLSFY.TSIYDHS.F.
Retrocopy NFTISKAYKVNIDMNFEVFIHKVDGLSDDYKI*TQRDIHQWANDDLADAGLEKLHLSFYFTSIYDHSTFA

Parental  AFSKVVQKL-IPQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVS
          AFSKV.QKL.IPQL..LE.LLN.FISNSGIEKAFLFDVVSKIYI.TDSSPVDMQS.ELCCDMID.VIDV.
Retrocopy AFSKVLQKL<IPQLLALEYLLNTFISNSGIEKAFLFDVVSKIYITTDSSPVDMQSQELCCDMIDIVIDVC

Parental  CIYGLKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFRKAIHEV
          C..GLKE..SGSAY.KES.AIIKLNNTTVLYLKEVTKFLALVCI.REESFE.K.LIDYNFHCFRKAIHEV
Retrocopy CMFGLKENRSGSAYHKESKAIIKLNNTTVLYLKEVTKFLALVCIHREESFE*KSLIDYNFHCFRKAIHEV

Parental  FEVGVTSHRSCSHQTSAPSLKALTHNGTPRNAI
          FEVGVTSHRSC.HQTS.P.LKALT.N.TP.N.I
Retrocopy FEVGVTSHRSCGHQTSVPNLKALTRNCTP*NVI

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	10.45 RPM
ERP005899_muscle	0.00 RPM	19.27 RPM
SRP017611_brain	0.00 RPM	19.28 RPM
SRP017611_kidney	0.00 RPM	29.52 RPM
SRP017611_liver	0.00 RPM	6.42 RPM
SRP030211_testis	0.01 RPM	22.26 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1023 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1023 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1023 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009368	2 retrocopies	retro_btau_1023 , retro_btau_851,
Bos taurus	ENSBTAG00000018438	1 retrocopy	retro_btau_1643,
Microcebus murinus	ENSMICG00000006241	1 retrocopy	retro_mmur_1581,
Monodelphis domestica	ENSMODG00000017710	1 retrocopy	retro_mdom_1967,