RetrogeneDB ID: retro_cpor_696

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_24:11658990..11659952(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDI2
• Ensembl ID: ENSCPOG00000013449
• Aliases: None
• Description: None

Sequence

>retro_cpor_696
GATGGTCATTTGGTTAAGATGCTCCTGTAAACAGAAATTATGTGATACATGGATTTCAAAGTGATTTAAGGCAGATTTTT
CTACAAGGAAAAGAATTATACAAGGTTCTCTTTACTAAAGTGGAAGCCCTGGTGTCTAGCTTAATGGGATTATTTTAAAA
ACATCACTTCAGAAAGTTCCTGTTTATGTTGCCAACTTTGATGAAAAAGACCCTAGAATTTTTTAGTGCATTGATCCTAA
GAAAACCATAATGCGAGATCTGTATAAGAAATTTGACTTGGCCCAAGATGTTATATATTTTCCTGGTCATTTTGCCACAC
TGTACAAACTGATGACTTTAGATCAGTCGTGTTGAGAGATCATTGATAGTATTAAACCTTACATTGAGTCTCCGGCAAGA
TATGGCAAAAGTCCATACCTTTACCCACTTTATGGCCTTGGAGAAGAACCACAAGCATTTGTCAGGCTAAGTGCTATTTA
TGGCAGTACCCACGTGTTGAATAAGCCAATTAAAGAAATGATTTGCAGAATGGAAAAGTGGTTGGTGTAAAATCTGAAGG
AGAGATAACTCATTGTAAGAAGCTCATCTGTGACCCAAATTATGCAAAGGATTGGATAGAATAAGTGGGCCAGGTGATTA
GAGTTATATGCATCCTCAGTCACCCCATCAGAAATACCAGTGATACCAGTTCCTGTCAGATAATTATTCCACAGAACCAA
GTCAATCAAAAATCAGATAGCTATGTTTATATGATCTTCTCTGCACACAATGTGGCAGCACAAGGGAAGTGCTGTGCCCA
TTGTTAGTACAAATGTGGAACCTGAGAAAGAAATCAGATCAGCTTTGGAGCTGTTGGAAACAACTGAATAAAAAATTGCT
AGCATCAGTGATCTCCTTGTACCAAAGATTTGGAAACAGACAGTCAGATTTTTATTTCCAGGCATATGATGCTCACTTTG
AG

Alignment

ORF - retro_cpor_696 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.65 %
• Parental protein coverage: 73.71 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  NGQLVKMLLYTEVTRYMDFKVIEGSFVYK-GGKIYKVSSTEAEALASSLMGLFEKRRFRKFL-VYVANFD
          .G.LVKMLL.TE...YMDFKVI.G.F.YK.G...YKV..T..EAL.SSLMGLF.K..FRKFL.VYVANFD
Retrocopy DGHLVKMLL*TEIM*YMDFKVI*GRFFYK<GKELYKVLFTKVEALVSSLMGLF*KHHFRKFL<VYVANFD

Parental  EKDPRTFEGIDPKKTTMRDLYKKFDLGQDVIDFTGHSLALYRTDDYLDQPCLETIDRIKLYSESLARYGK
          EKDPR.F..IDPKKT.MRDLYKKFDL.QDVI.F.GH...LY.....LDQ.C.E.ID.IK.Y.ES.ARYGK
Retrocopy EKDPRIF*CIDPKKTIMRDLYKKFDLAQDVIYFPGHFATLYKLMT-LDQSC*EIIDSIKPYIESPARYGK

Parental  SPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEII-VQNGKVVGVKSEGEIARCKQLICDPSYVKDR
          SPYLYPLYGLGE.PQ.F.RLSAIYG.T..LNKPI.E.I..QNGKVVGVKSEGEI..CK.LICDP.Y.KD.
Retrocopy SPYLYPLYGLGEEPQAFVRLSAIYGSTHVLNKPIKEMI<LQNGKVVGVKSEGEITHCKKLICDPNYAKDW

Parental  VEKVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISSAHNVAAQGKYIA-IVSTTVET
          .E.VGQVIRVICILSHPI.NT.D..SCQIIIPQNQVN.KSD.YV.MI.SAHNVAAQGK..A.IVST.VE.
Retrocopy IE*VGQVIRVICILSHPIRNTSDTSSCQIIIPQNQVNQKSDSYVYMIFSAHNVAAQGKCCA>IVSTNVE-

Parental  KEPEKEIRPALELLEPIEQKFVSISDLLVP-KDLGTDSQIFISR-AYDATTHFE
          ..PEKEIR.ALELLE..E.K..SISDLLVP.KDL.TDSQIFISR.AYDA..HFE
Retrocopy --PEKEIRSALELLETTE*KIASISDLLVP<KDLETDSQIFISR<AYDA--HFE

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	95.42 RPM
SRP017611_kidney	0.00 RPM	149.70 RPM
SRP017611_liver	0.00 RPM	149.56 RPM
SRP040447_lung	0.00 RPM	105.04 RPM
SRP040447_skeletal_muscle	0.00 RPM	59.09 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_696 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_696 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196, retro_cfam_886,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696 ,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,