RetrogeneDB ID: retro_btau_1671

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 9:31895269..31896319(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000039169
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GPD1L
• Ensembl ID: ENSBTAG00000009826
• Aliases: None
• Description: glycerol-3-phosphate dehydrogenase 1-like protein [Source:RefSeq peptide;Acc:NP_001093833]

Sequence

>retro_btau_1671
ATGACAGAATCACCCCTGAAAGTTTGCATCGTGGGCTCGGGGAACTGGGGTTCAGCTATTGCAAAAATAATTGGTAATAA
TGTCATGAAACTTCAGAAGTTTGCCTCCACGGTCAAGATGTGGGTCTTTGAAGAAATGGTTAATGGGAGAAAACTAATAG
ACATCATAAATAACGACCATGAAAATGTAAAATATCTCCCTGGACACAAGCTGCCAGACAATGTGATTGCAGTCCCCAAC
CTCAGTGAGGCTGTGTGGGATGCAGACCTGCTGGTGTTTGTGATCCCCCACCAGTTCATCAACAGCATCTGCGAGGAGAT
CTCTGGGAAAGTGCCCAAGGGCGCCCTGGGCATCAGCCTCATCAAGGGCATAGATGAGGGTCCCCAGGGGCTGAAGCTCA
TTTCTGACATCATCCGAGAGAAGATGGACATTGACGTCAGTGTGCTGATGGGCGCCAACACTGCCAATGAGGTGGCTGCC
GAGAAGTTCTGTGAGACCACCATCGGCAGCAAGGTAATGGAGCACGGCCTCCTCTTCAAAGAACTTCTTCAGACTCCAAA
TTTTCGAATTAAGGTGGTTGCTGAGGCAGACGCTGTTGAACTTTGTGGCGCTCTGAAGAACATTGTGGCCGTGGGAGCCG
GGTTCTGCGACGGCCTCCACTGCGGCGACAACACCAAAGCTGCCGTCATCCGCCTGGGGCTCATGGAAATGATCACCTTC
GCCAGGATCTTCTGCAAGGGCCACGTGTCCAAAGCCACCTTCCTGGAGAGCTGCGGCGTGGCCGACCTGATCACTACCTG
CTACGCGGGCCGGAACCGCAAGGTAGCTGAGGCCTTTGCGGCGACCGGAAAGACCATTGAAGAACTGGAGAAGGAGATGC
TGAACGGGCAGAAGCTGCAAGGACCACAGACTTCCGCCGAGGTGTATGGCATCCTCAAACCGAAGGGACTGCTGGACAAG
TTTCCATTGTTCACGGCGGTGTACCAGATCTGCTACGAAGGCAGGCCTGTTGAAGAGATGTTGTCTTGTCTCCAGAATCA
TCCGGAGTAT

Alignment

ORF - retro_btau_1671 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.57 %
• Parental protein coverage: 99.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAPLKVCIVGSGNWGSAVAKIIGNNVRKLQKFASTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHK
          M...PLKVCIVGSGNWGSA.AKIIGNNV.KLQKFASTVKMWVFEE.VNGRKL.DIINNDHENVKYLPGHK
Retrocopy MTESPLKVCIVGSGNWGSAIAKIIGNNVMKLQKFASTVKMWVFEEMVNGRKLIDIINNDHENVKYLPGHK

Parental  LPENVVAVANLSEAVQDADLLVFVIPHQFIHRICDEITGRVPKDALGITLIKGIDEGPEGLKLISDIIRE
          LP.NV.AV.NLSEAV.DADLLVFVIPHQFI..IC.EI.G.VPK.ALGI.LIKGIDEGP.GLKLISDIIRE
Retrocopy LPDNVIAVPNLSEAVWDADLLVFVIPHQFINSICEEISGKVPKGALGISLIKGIDEGPQGLKLISDIIRE

Parental  KMGIDISVLMGANIANEVAAGKFCETTIGSKIMENGLLFKELLQTPNFRITVVDDADTVELCGALKNIVA
          KM.ID.SVLMGAN.ANEVAA.KFCETTIGSK.ME.GLLFKELLQTPNFRI.VV..AD.VELCGALKNIVA
Retrocopy KMDIDVSVLMGANTANEVAAEKFCETTIGSKVMEHGLLFKELLQTPNFRIKVVAEADAVELCGALKNIVA

Parental  VGAGFCDGLLCGDNTKAAVIRLGLMEMIAFARIFCKGQVSTATFLESCGVADLITTCYGGRNRKVAEAFA
          VGAGFCDGL.CGDNTKAAVIRLGLMEMI.FARIFCKG.VS.ATFLESCGVADLITTCY.GRNRKVAEAFA
Retrocopy VGAGFCDGLHCGDNTKAAVIRLGLMEMITFARIFCKGHVSKATFLESCGVADLITTCYAGRNRKVAEAFA

Parental  RTGKTIEELEKEMLNGQKLQGPQTSAEVYRILKQKGLLDKFPLFTAVYQICYEGRPVQEMLSCLQSHPEH
          .TGKTIEELEKEMLNGQKLQGPQTSAEVY.ILK.KGLLDKFPLFTAVYQICYEGRPV.EMLSCLQ.HPE.
Retrocopy ATGKTIEELEKEMLNGQKLQGPQTSAEVYGILKPKGLLDKFPLFTAVYQICYEGRPVEEMLSCLQNHPEY

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	0.29 RPM
ERP005899_muscle	0.00 RPM	34.84 RPM
SRP017611_brain	0.00 RPM	8.72 RPM
SRP017611_kidney	0.00 RPM	10.91 RPM
SRP017611_liver	0.00 RPM	0.76 RPM
SRP030211_testis	4.43 RPM	17.71 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1671 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1671 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1671 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_154

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009826	1 retrocopy	retro_btau_1671 ,
Choloepus hoffmanni	ENSCHOG00000012633	5 retrocopies	retro_chof_1033, retro_chof_306, retro_chof_340, retro_chof_620, retro_chof_724,
Loxodonta africana	ENSLAFG00000013996	1 retrocopy	retro_lafr_101,
Microcebus murinus	ENSMICG00000011060	1 retrocopy	retro_mmur_1205,
Mus musculus	ENSMUSG00000050627	3 retrocopies	retro_mmus_1348, retro_mmus_2552, retro_mmus_3695,
Oryctolagus cuniculus	ENSOCUG00000010093	2 retrocopies	retro_ocun_1529, retro_ocun_1588,
Otolemur garnettii	ENSOGAG00000013243	1 retrocopy	retro_ogar_285,
Procavia capensis	ENSPCAG00000016132	1 retrocopy	retro_pcap_316,
Rattus norvegicus	ENSRNOG00000026455	2 retrocopies	retro_rnor_2035, retro_rnor_2474,
Sus scrofa	ENSSSCG00000021977	1 retrocopy	retro_sscr_154,