RetrogeneDB ID: retro_btau_1643

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:31024166..31025238(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RRAGD
• Ensembl ID: ENSBTAG00000018438
• Aliases: None
• Description: ras-related GTP-binding protein D [Source:RefSeq peptide;Acc:NP_001179757]

Sequence

>retro_btau_1643
GAGGAGGAGGATGAGCTGATGGGGCTAGTGGACCACGGAGACGGGTCCCACTCCTCTGACGCCAAGCTGGACACCGGGGC
GGAGGAGGGAGTTCTGGACGTTAGCGACCCGCTTAGCACAGAGGTCAAGCCAAGGATCCTGCACACAGGCCTAAGAAGGA
GCGGCAAGTCATCCATCCAGAAAGTCGTCTTTCATAAAATGTTTCCCAGGGAAACTCTGTTCTTGGAGAGCACGAAGAAG
ATCTGTTGGGAGGACGTTTCCAACAGTTTCTTTGTTAATTTTCAGATTTGGGACTTTCCAGGACAGATTGACTTTTTTGA
CCCCACCTTTGACTACGAGATGATCTTCCAAGAGACGGGAGCACTGATATTTGTCATAGACTCCCAGGACGATTACATGG
AGGCCTTGGCCAGATCCACCTCACAGTGACCACGGCCTACAAAGTCAACAGCGACATAAACTTTGAGGTGTTTATTCACA
AAGTGGATGGGTCTATCAGATGACACAAAATTTAAACCCAGAGAGACATTCACCAGAGGGCAAATGATGCCCTTGCAGAT
GCTAGGCTAGAAAAAATTCATGTCAGCTTTTATTTGACAAGCATATATGACCATTCAATATTTGAAGCTTTTGGCAAAGT
GGTTCAGAAACTGATTCCACAACTTCCCACCCTGGAGAATTTGCTAAACATCTTTATCTCAAATTTTGGGATTGAAAAGT
TGTTTCTCTTTGATGTGGTCGGTAAGATTTATATCACAACAGACAGTACCCCTGTGAATATGCAAACCTAGGAGCTCTGC
TGTGACATGATGATGTGGTCATTGATATTTCTTGTATTTGTGGCCTCAAAGAAGATGGAGCAGGAACCCCCTATAACAAG
GAATCAACAGCCATTATAAAGCTGAATAATACAACAGTTCTTTATTTAAAAGAGGCGACAAAGTTTCTGGCTCTTTTTTG
CTTTGTTAGAGAGGAAAGCTTTGAAAGAAAAGGTCTGATTGACTATAATTTTCATTGCTTCCGGAAGGCCATCCATGAAG
TTTTTGAGGTGAAGTTGCGAAAGGTTCAGAAT

Alignment

ORF - retro_btau_1643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 90.18 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EEEDELVGLADYGDGPDSSDAEPDSGAEEGVLDFSDPFSTEVKPRILLMGLRRSGKSSIQKVVFHKMSPN
          EEEDEL.GL.D.GDG..SSDA..D.GAEEGVLD.SDP.STEVKPRIL..GLRRSGKSSIQKVVFHKM.P.
Retrocopy EEEDELMGLVDHGDGSHSSDAKLDTGAEEGVLDVSDPLSTEVKPRILHTGLRRSGKSSIQKVVFHKMFPR

Parental  ETLFLESTNKICREDVSNSSFVNFQIWDFPGQIDFFDPTFDYEMIFRGTGALIFVIDSQDDYMEALAR-L
          ETLFLEST.KIC.EDVSNS.FVNFQIWDFPGQIDFFDPTFDYEMIF..TGALIFVIDSQDDYMEALAR..
Retrocopy ETLFLESTKKICWEDVSNSFFVNFQIWDFPGQIDFFDPTFDYEMIFQETGALIFVIDSQDDYMEALAR<I

Parental  HLTVTRAYKVNTDINFEVFIHKVDGLSDDHKIETQRDIHQRANDDLADAGLEKIHLSFYLTSIYDHSIFE
          HLTVT.AYKVN.DINFEVFIHKVDG....HKI.TQRDIHQRAND.LADA.LEKIH.SFYLTSIYDHSIFE
Retrocopy HLTVTTAYKVNSDINFEVFIHKVDGSIR*HKI*TQRDIHQRANDALADARLEKIHVSFYLTSIYDHSIFE

Parental  AFSKVVQKLIPQLPTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSTPVDMQTYELCCDMI-DVVIDIS
          AF.KVVQKLIPQLPTLENLLNIFISN.GIEK.FLFDVV.KIYI.TDSTPV.MQT.ELCCDM..DVVIDIS
Retrocopy AFGKVVQKLIPQLPTLENLLNIFISNFGIEKLFLFDVVGKIYITTDSTPVNMQT*ELCCDMM<DVVIDIS

Parental  CIYGLKEDGAGTPYDKESTAIIKLNNTTVLYLKEVTKFLALVCFVREESFERKGLIDYNFHCFRKAIHEV
          CI.GLKEDGAGTPY.KESTAIIKLNNTTVLYLKE.TKFLAL.CFVREESFERKGLIDYNFHCFRKAIHEV
Retrocopy CICGLKEDGAGTPYNKESTAIIKLNNTTVLYLKEATKFLALFCFVREESFERKGLIDYNFHCFRKAIHEV

Parental  FEVRMKVVKS
          FEV....V..
Retrocopy FEVKLRKVQN

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	1.01 RPM
ERP005899_muscle	0.00 RPM	2.16 RPM
SRP017611_brain	0.00 RPM	20.78 RPM
SRP017611_kidney	0.00 RPM	37.46 RPM
SRP017611_liver	0.00 RPM	1.28 RPM
SRP030211_testis	0.00 RPM	11.16 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1643 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1643 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1643 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 ,
Choloepus hoffmanni	ENSCHOG00000001038	1 retrocopy	retro_chof_301,
Equus caballus	ENSECAG00000015826	1 retrocopy	retro_ecab_558,