RetrogeneDB ID: retro_cpor_1546

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_97:4991618..4992681(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUV39H2
• Ensembl ID: ENSCPOG00000008492
• Aliases: None
• Description: None

Sequence

>retro_cpor_1546
GACCTGAGGCTCAAGGAGGATGTGGAATACTATCATGTAAAATGGGAAATCTGGGCAGATTCTACAAACATTTGGGAATC
TTGGCAAAATTTCAAATGTGCATTACTGCTTCAGCAATTCATTAATGACACATATAATTATATATGTCAGATAAAGAAAA
GCAAAGCAATAATTCCAAAAGACAGCAATAAAACTTTGAGACCTACTGTTGTTCAGTACATTATAAAGAAAGCTAAACAA
AGAAAAGCTCTGCAAAAGTGGTAAGATGAACTCAAAAGAAAGAATTGTAAAGGAATGATATTTGTTGGAAATACTGTTGA
TTTAGAGAGTCCACCTACAGACTTCCCCTACATTATAGAATACAAACCAGCTCCTGGAATCAGTTTAGTCAATGAAGTGA
CCTTTAGTTTTTCATGCACGGATTACTGCTTTGCGAAATATTGTCCTACTGAAGCTGGCATTGTTTTGCATATAATAAGA
AATGACATATTAAAATACCACCTAGTACTCCCATCTATGAATGCAATTCAAGATTCCTGGTGGACCCAATTGCCCCAATA
GAATTGTACAGAAAGGTACATGGCATTCACTTTGCATCTTTTGAACAAGCAACGGCTGTGGCTGCGGTGTAAAGACTCGT
GAAGAATAAAATAATGGGTTTTATCATGAAATATTTTGAAGAGGTAAGCGTAAGTGAAAGAGCTGCAATATGGGGACAGT
TATATAACAACAAAGAGCTAATTTATCTCTTTGATCTGGATTATGAATCTGATGAATCACAGTGGATGCAGCTTGATAAG
GAAATATGTTTCAGTGTGTGATTCATAGCTCTGACTCAAATCTTCAAGTATTTAATGCTTTCATCAATAACCTCAAAACT
CATCTTCCTCAAATAGTATTGTTTTCTCCAAGAACCATATATGCTGGAGAACAGCTAACTCTTGATTAGCACATGAAAGA
ATCTGGAGATATGTATTCAGACTCTGTTGACCACAAACCAGCAAGACACAGGGTCGGAACTGTGTGCAGCTGTGGGGTGG
CGATGTGTAGAGGTTAGCTCAAT

Alignment

ORF - retro_cpor_1546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.23 %
• Parental protein coverage: 87.07 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DYKVVKDMEYYLVKWKGWPDSTNTWEPLQNLKCPLLLQQFSNDKHNYLSQVKKSKAIIPKDNNKTLRPAI
          D.....D.EYY.VKW..W.DSTN.WE..QN.KC.LLLQQF.ND..NY..Q.KKSKAIIPKD.NKTLRP..
Retrocopy DLRLKEDVEYYHVKWEIWADSTNIWESWQNFKCALLLQQFINDTYNYICQIKKSKAIIPKDSNKTLRPTV

Parental  ARYIVKKAKQRIALQKWQDELNRRKNHKGMIFVENTVDLEGPPTDFYYINEYKPAPGISLVSEVTFGCSC
          ..YI.KKAKQR.ALQKW.DEL..RKN.KGMIFV.NTVDLE.PPTDF.YI.EYKPAPGISLV.EVTF..SC
Retrocopy VQYIIKKAKQRKALQKW*DEL-KRKNCKGMIFVGNTVDLESPPTDFPYIIEYKPAPGISLVNEVTFSFSC

Parental  TDCFLEKCCPTEAGVVL-AYNKNQQIKIPPGTPIYECNSRCQCGPDCPNRIVQKGTQYSLCIFRTSNGCG
          TD....K.CPTEAG.VL.AYNK...IKIPP.TPIYECNSR....P..P.....K........F.......
Retrocopy TDYCFAKYCPTEAGIVL<AYNKK*HIKIPPSTPIYECNSRFLVDPIAPIELYRKVHGIHFASFEQATAVA

Parental  WGVKTLVKIKRMSFVMEYVGEVITSEEAERRGQLYDNKGITYLFDLDYESDE-FTVDAARYGNVSHFVNH
          ..V..LVK.K.M.F.M.Y..EV..SE.A...GQLY.NK...YLFDLDYESDE..TVDAA..GN....V.H
Retrocopy -AV*RLVKNKIMGFIMKYFEEVSVSERAAIWGQLYNNKELIYLFDLDYESDE<ITVDAA**GNMFQCVIH

Parental  SCDPNLQVFNVFIDNLDTRLPRIALFSTRTIYAGEELTFDYQMKGSGDTSSDSIDHSPAKKRVRTVCKCG
          S.D.NLQVFN.FI.NL.T.LP.I.LFS.RTIYAGE.LT.D..MK.SGD..SDS.DH.PA..RV.TVC.CG
Retrocopy SSDSNLQVFNAFINNLKTHLPQIVLFSPRTIYAGEQLTLD*HMKESGDMYSDSVDHKPARHRVGTVCSCG

Parental  AVTCRGYLN
          ...CRG.LN
Retrocopy VAMCRG*LN

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	3.68 RPM
SRP017611_kidney	0.00 RPM	5.97 RPM
SRP017611_liver	0.00 RPM	2.87 RPM
SRP040447_lung	0.00 RPM	3.78 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1546 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1546 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004696	1 retrocopy	retro_cfam_574,
Cavia porcellus	ENSCPOG00000008492	1 retrocopy	retro_cpor_1546 ,
Homo sapiens	ENSG00000152455	1 retrocopy	retro_hsap_3482,
Gorilla gorilla	ENSGGOG00000028243	1 retrocopy	retro_ggor_2348,
Microcebus murinus	ENSMICG00000002803	1 retrocopy	retro_mmur_340,
Nomascus leucogenys	ENSNLEG00000012108	1 retrocopy	retro_nleu_2202,
Oryctolagus cuniculus	ENSOCUG00000015090	1 retrocopy	retro_ocun_1408,
Ochotona princeps	ENSOPRG00000009465	1 retrocopy	retro_opri_1005,
Pongo abelii	ENSPPYG00000002106	1 retrocopy	retro_pabe_2877,
Tupaia belangeri	ENSTBEG00000006477	4 retrocopies	retro_tbel_2646, retro_tbel_3572, retro_tbel_852, retro_tbel_993,