RetrogeneDB ID: retro_rnor_2474

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:101278595..101279648(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000004906
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Gpd1l
• Ensembl ID: ENSRNOG00000026455
• Aliases: None
• Description: glycerol-3-phosphate dehydrogenase 1-like protein [Source:RefSeq peptide;Acc:NP_001178814]

Sequence

>retro_rnor_2474
ATGGGTGCTACAACCCTGAGAGTGTGCATTGTAGGCTTCTGGAGTTGGGGATCAGCTATTGCAAAAATAATTGGGACTAA
TGTCAAGAACCAGCAGAAGTTCGCCTCCACAGTCAAGATGTGGGTCTCTGAAGAAGCAGTGAACGGGAGGAAACTGACAG
ACATCATAAATCACTACCATGAAAACGTCAAATATCTTCCAGGACATAAGCTGCCAGAAAATGTGGTTGCTGTCGCAAAT
CTCAGTGAGGCAGTGCAGGATGCAGATCTACTGGTGTTCACCACCCCACACCAGTTCATTCACAAAATCTGTAATGAGAT
TACTGGCAGGGTGCCCAAGAAGGCTCTTGGCATCATTCACATGGAGAGCATAGATGAGGGCCCGAGAGGACTGATGCTCA
TTTCCGACATCATTCGAGAGAAGATAGGGATGGACGTTAGCGTGCTGATGGGGGCTAATACAGCCAGGGAGGTGGCTGCT
GGGGAGTTTTGTGAGACTACCATTGGTAGCAAAGTTATTCAGAATGGCATTCTCTTCAAAGAGCTGCTTCAGACCTCCAA
CTTCTGCATCACTGTGGTGGATGATGCTGATGCCGTGGAACTCTGCGGAGCACTAAAACACATCGTTGCCATGGGAACCA
ACTTCTGCAATGGCCTCCACTGCGGGAACAACAGCAAGGCAGCTGTCCTCCGCCTTGGCCTTGTAGAAATGATCACTTTC
ACCAGGATCTTCTGCAAGAGCCAGGTGTCCACGACCACCTTCCTTGAGAGCTGTGGCTTTGCCAACCCCATCACTATCTG
CTACAGAGGGAGTGACTGCAAGGAGGCTAAGACCTTCCCCAGGATTGGGAAGACTATGGGAAACCTACAAAAGGAAGTGC
TGAATGGTCAGACACTTCAAGGACTTAAGACCTCTGCTTTAGTGTACCAATTCCTCAAGCAGAAGGGGCTTCTAGCTAAG
TTTCCATTATTTGTAACAGTGTATCGGATCTGTTATGAAGGCAGACCTTCCACAGAGATACTAACCTGCCTCCAGAACCA
TCCTGCACACATG

Alignment

ORF - retro_rnor_2474 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAPLKVCIVGSGNWGSAVAKIIGSNVKNLQKFSSTVKMWVFEETVNGRKLTDIINNDHENVKYLPGHK
          M.A..L.VCIVG...WGSA.AKIIG.NVKN.QKF.STVKMWV.EE.VNGRKLTDIIN..HENVKYLPGHK
Retrocopy MGATTLRVCIVGFWSWGSAIAKIIGTNVKNQQKFASTVKMWVSEEAVNGRKLTDIINHYHENVKYLPGHK

Parental  LPENVVAVPNLGEAVQDADLLVFVIPHQFIHKICDEITGRVPKKAVGITLIKGIDEGPDGLKLISDIIRE
          LPENVVAV.NL.EAVQDADLLVF..PHQFIHKIC.EITGRVPKKA.GI.....IDEGP.GL.LISDIIRE
Retrocopy LPENVVAVANLSEAVQDADLLVFTTPHQFIHKICNEITGRVPKKALGIIHMESIDEGPRGLMLISDIIRE

Parental  KMGIDISVLMGANIASEVAAEKFCETTIGSKVLQNGLLFKELLQTPNFRITVVDDADTVELCGALKNIVA
          K.G.D.SVLMGAN.A.EVAA..FCETTIGSKV.QNG.LFKELLQT.NF.ITVVDDAD.VELCGALK.IVA
Retrocopy KIGMDVSVLMGANTAREVAAGEFCETTIGSKVIQNGILFKELLQTSNFCITVVDDADAVELCGALKHIVA

Parental  VGAGFCDGLCCGDNTKAAVIRLGLMEMIAFAKIFCKGQVSTATFLESCGVADLITTCYGGRNRKVAEAFA
          .G..FC.GL.CG.N.KAAV.RLGL.EMI.F..IFCK.QVST.TFLESCG.A..IT.CY.G...K.A..F.
Retrocopy MGTNFCNGLHCGNNSKAAVLRLGLVEMITFTRIFCKSQVSTTTFLESCGFANPITICYRGSDCKEAKTFP

Parental  RTGKTIEELEKELLNGQKLQGPQTSAEVYRILKQKGLLDKFPLFTAVYQICYEGRPVTQMLSCLQSHPEH
          R.GKT...L.KE.LNGQ.LQG..TSA.VY..LKQKGLL.KFPLF..VY.ICYEGRP.T..L.CLQ.HP.H
Retrocopy RIGKTMGNLQKEVLNGQTLQGLKTSALVYQFLKQKGLLAKFPLFVTVYRICYEGRPSTEILTCLQNHPAH

Parental  I
          .
Retrocopy M

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
SRP017611_brain	0.00 RPM	82.03 RPM
SRP017611_kidney	0.00 RPM	105.58 RPM
SRP017611_liver	0.00 RPM	14.79 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2474 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2474 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2474 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_1348

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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,