RetrogeneDB ID: retro_btau_498

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 12:38893852..38894353(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK1
• Ensembl ID: ENSBTAG00000010312
• Aliases: MAPK1, ERK2
• Description: Mitogen-activated protein kinase 1 [Source:UniProtKB/Swiss-Prot;Acc:P46196]

Sequence

>retro_btau_498
CACATAGAGTTCCAGACAGGGAATATGGCCAATCGCTGGTAGTGGGCTCCAGAAATCATGTTGAACTCCAAGGGCTACAC
CAAGTCTATTGACATCTGGTCTGTGGGCTGCATCCTGGCAGAGATACTCTCCAACAGACCCATCTTCCCCAGGAAGCATT
ACCTCGACCAGCTGAAACACGTTCTGAGTATTCTTGGATCCTTATCTCAGAAAAACCTAAATTGTATAAAAAATTTAAAA
GCTAGAAACTATCTTCTCTCTCTTCCACACAAAAATAAGGAGCCATGGAACAGGCTGTTCCCAAATGTTGACGCCAAAGC
TCTGGATTTACTGGACAAAATGTTGGCATTCAACCCTCACAAGAAGATTGAGGTGGAGCAGGCTCTGGCCCACCTGTCCC
TGGAGCAGTGCTAGGACCCGAGTGATGAGCCCATCACTGAAGCACCCTTCACGTTTGACATGGAATTGGATGACTTGCCC
AAGAAAAAGCTCAAAGAACTC

Alignment

ORF - retro_btau_498 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.44 %
• Parental protein coverage: 52.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQ
          H..F.T...A.RW..APEIMLNSKGYTKSIDIWSVGCILAE.LSNRPIFP.KHYLDQL.H.L.ILGS.SQ
Retrocopy HIEFQTGNMANRW*WAPEIMLNSKGYTKSIDIWSVGCILAEILSNRPIFPRKHYLDQLKHVLSILGSLSQ

Parental  EDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDP
          ..LNCI.NLKARNYLLSLPHKNK.PWNRLFPN.D.KALDLLDKML.FNPHK.IEVEQALAH..LEQ..DP
Retrocopy KNLNCIKNLKARNYLLSLPHKNKEPWNRLFPNVDAKALDLLDKMLAFNPHKKIEVEQALAHLSLEQC*DP

Parental  SDEPVAEAPFKFDMELDDLPKEKLKEL
          SDEP..EAPF.FDMELDDLPK.KLKEL
Retrocopy SDEPITEAPFTFDMELDDLPKKKLKEL

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	6.13 RPM
ERP005899_muscle	0.00 RPM	26.18 RPM
SRP017611_brain	0.00 RPM	139.19 RPM
SRP017611_kidney	0.00 RPM	43.92 RPM
SRP017611_liver	0.00 RPM	17.67 RPM
SRP030211_testis	0.00 RPM	61.71 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_498 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_498 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_498 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010312	1 retrocopy	retro_btau_498 ,
Ficedula albicollis	ENSFALG00000007935	1 retrocopy	retro_falb_19,
Gallus gallus	ENSGALG00000001501	1 retrocopy	retro_ggal_20,
Myotis lucifugus	ENSMLUG00000005952	1 retrocopy	retro_mluc_302,
Monodelphis domestica	ENSMODG00000017722	1 retrocopy	retro_mdom_101,
Ochotona princeps	ENSOPRG00000014484	2 retrocopies	retro_opri_242, retro_opri_615,