RetrogeneDB ID: retro_cpor_281

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_116:3566109..3567239(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KIN
• Ensembl ID: ENSCPOG00000010515
• Aliases: None
• Description: None

Sequence

>retro_cpor_281
ATGGTGAAGTCAGACTTTCTTATCCCCAAGACCATTGCCAACTGGATTCAATGCAATGGATTTCAAAAGCAGCCCTGGTG
TTCCCAGATATGACATAAGCAATGCCAGGATGAGAATGGCTTTCAGGGTCACTGCATGTCAGAATGTAATCAGACACAAC
TATTGCTGGCTTCAGAAAATCCTCAGCAGTGGATGGATTGTTTTTCAGAGGAATCCCACAGTGACTTAGAAATTCTCAGA
AGATGATTTGGCACCTGGAAAGTCTATAATAATCTGCTGTACAATCAGTACATCAGGCCCTGAGAGACTCTCAATATGAA
CACTGCTGAGTGGGAAATGCTGATAGACTTCACTAAGTGGCTAGGCAGACAAGGCCTATGCAAAGTGGATAAGACCCCCT
AAGGCTGGTATATTCAGTACATCAACAAGGAGACCACCCACTGGCAGATCAAGATAGGCAAGAAGAAGAAGCAGAAACTT
GCCAATGAAGAAAAATGTGCACAATGATTGAGGAACAATTGCAAAGAGGTCTGAAAAGGAAGGAGCAAGAGGCCCTGTCT
TTATGGAATTCTAAGAGAAAAGGATGAAGAGAAAGTTACCTTTCTTCTGAAGAAAGGAGCACTTATTTCAGCAGGACCCA
CATCATGCAAATCCAGTTCTTTGGGGCCAAGTGCACTGAAGATGCTTGGGATAATGGCATCAGTGAAACAACAACAACAA
CAAAAAACTTTCCAGAGTTCAGCTCAGCCTCAAGAAAATAAAAGGAAATGAGCACTTGAAGAAATCATGGAGACTGAAGA
GGAAAAGAAAAGAACATTTTAAATAGAGTATTGGCTAAAGCCTGAAATCACTGTGAAAATTAGAACCAAAAATCTTGCAG
AGAAACCCCATCAGAAAAAGGATGTGGTTAAGGAGGTCATTGACAAATACACAGTCATGGTCAAGATGACTGATTCTAGA
GACCAGCTGAAACTTGACTAGAATCCTTTAGAGATAGGCATTGCAGGACGGGCAAAACAATTCCAGTTTTAAATGCAGGT
TACAGGGGAAATGAAGGGACTCTGGAATCCATCAGTGAAAAGACTTTCTCAACTACAATAATCATTGAAACTGGCCCTGT
CAAAGGACAG

Alignment

ORF - retro_cpor_281 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.99 %
• Parental protein coverage: 96.44 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGKSDFLTPKAIANRIKSKGLQKLRWYCQMCQKQCRDENGFKCHCMSESHQRQLLLASENPQQFMDYFSE
          M.KSDFL.PK.IAN.I...G.QK..W..Q...KQC.DENGF..HCMSE..Q.QLLLASENPQQ.MD.FSE
Retrocopy MVKSDFLIPKTIANWIQCNGFQKQPWCSQI*HKQCQDENGFQGHCMSECNQTQLLLASENPQQWMDCFSE

Parental  EFRNDFLELLRRRFGTKRVHNNIVYNEYISHREHIHMNATQWETLTDFTKWLGREGLCKVDETPKGWYIQ
          E...D.LE.LRR.FGT..V.NN..YN.YI...E...MN...WE.L.DFTKWLGR.GLCKVD.TP.GWYIQ
Retrocopy ESHSD-LEILRR*FGTWKVYNNLLYNQYIRP*ETLNMNTAEWEMLIDFTKWLGRQGLCKVDKTP*GWYIQ

Parental  YIDRDPETIRRQLELEKKKKQDLDDEEKTAK-FIEEQVRRGLEGKEQEA-PVFTE-LSRENDEEKVTFNL
          YI....ET...Q....KKKKQ.L..EEK.A...IEEQ..RGL..KEQEA.PVF.E...RE.DEEKVTF.L
Retrocopy YINK--ETTHWQIKIGKKKKQKLANEEKCAQ<MIEEQLQRGLKRKEQEA<PVFME<ILREKDEEKVTFLL

Parental  NKGACSSSGATTSKSSSLGPSALKTLGSTASVKRKE---TSQSSAQSKEKKKKKSALDEIMEIEEEKKRT
          .KGA..S.G.T..KSSSLGPSALK.LG..ASVK......T.QSSAQ..E..K.K.AL.EIME.EEEKKRT
Retrocopy KKGALISAGPTSCKSSSLGPSALKMLGIMASVKQQQQQKTFQSSAQPQE-NKRK*ALEEIMETEEEKKRT

Parental  SRTDYWLQPEIIVKIITKKLGEKYHKKKGIVKEVIDRYTAVVKMIDSGDKLKLDQTHLETVIPA-PGKRI
          ....YWL.PEI.VKI.TK.L.EK.H.KK..VKEVID.YT..VKM.DS.D.LKLD...LE..I....GK.I
Retrocopy F*IEYWLKPEITVKIRTKNLAEKPHQKKDVVKEVIDKYTVMVKMTDSRDQLKLD*NPLEIGIAG<TGKTI

Parental  LVLNGGYRGNEGTLESINEKTFSATIVIETGPLKGR
          .VLN.GYRGNEGTLESI.EKTFS.TI.IETGP.KG.
Retrocopy PVLNAGYRGNEGTLESISEKTFSTTIIIETGPVKGQ

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	6.67 RPM
SRP017611_kidney	0.00 RPM	6.07 RPM
SRP017611_liver	0.00 RPM	3.92 RPM
SRP040447_lung	0.00 RPM	6.71 RPM
SRP040447_skeletal_muscle	0.00 RPM	2.37 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_281 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_281 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004280	1 retrocopy	retro_acar_162,
Cavia porcellus	ENSCPOG00000010515	5 retrocopies	retro_cpor_279, retro_cpor_281 , retro_cpor_818, retro_cpor_987, retro_cpor_989,
Dipodomys ordii	ENSDORG00000003732	2 retrocopies	retro_dord_344, retro_dord_657,
Ficedula albicollis	ENSFALG00000001842	1 retrocopy	retro_falb_26,
Myotis lucifugus	ENSMLUG00000002261	1 retrocopy	retro_mluc_1186,
Rattus norvegicus	ENSRNOG00000026690	1 retrocopy	retro_rnor_2665,
Taeniopygia guttata	ENSTGUG00000002119	1 retrocopy	retro_tgut_9,