RetrogeneDB ID: retro_cpor_818

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_296:93569..94744(-)
• 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_818
ATCGGGAAGTCAGACTTTGTTATCCCCAGGACCATCTCCAACTGGATTCAATGCAAGGTGTTTCAAAAGCTGCCCTGGTG
TTGCCAGATATGACAGAAGCAATGCCAGGATGAGAATGGCTTTCAGGATTATTGCATGTCAGAATAAAATCAGACACAAC
TATTGTTGGCTTCAGAACATTCTCAGCAGTGGACGGATTGTTTTTCAGAGAAATCCCACAGTGACTTAGAAATTCTCAGA
AGATGATTTGGCACCTGTCAAGTCCATAACAATCTAGTGTGCAATCAGTTCATCAGACACCAAGAACACAGTGTTACATA
TGAACACTCTGCTGAGTGGGAAATGCTGATGGACTTCACTAAGTGGCAGGGCAGACAAGGCCTGTGCAAAGTGGATGAGA
CCCCTAAGACTGGTATATTCAGTACATCAGCTGGGACCCAGAGACCAGCCAGTGGCAGATGGAACTAGGCAAGAAGAAGA
AACAGAACCTTGACAGTGAAGAAAAATGGGCAAATTGATTGAGAAACAAGTGCAACAAGGTCTGAAAAGGAAGGACCAAG
AGGTCCTGTCTTTATGGAATTTGAAGAGGAAAAGATAAAGTGAAAGTTACCTTTGTTCTGGAGCAAGGAGCACCTATTTC
AGCAGGATCCTCATCATCCAAAACCAGTTCTTTAGGGCCAAGTTCACTGAAGATGCTTCGGAGAATGGCATCAGTAAAAC
AAAAAGAAACTTTCCAGAGCTCAGCTCGGTCTCAAGAAAAGAAAAAGAAATCTTCAATTGAAGAAATCATGGAGAGTGAA
GAGGAAAGGAAAAGAAAACCTCATACAGAGTATTGGTTACAACCTAAAATCACTGTGAAAATTAGAACCAACAATCTTGC
AGTGAATTCCCATCAGAAAAATGGTGTGGATATGGAGGTAATTAATAAATACACAGCCATTGTCAAGTTGATTGATTCTA
GAGACCAACTGAAGCTTTACCAGAGTCCTTTAGAGACAGGCAATGCAGGACAGGGAAAAATAATTTCAGTTTTAAATGCA
AGTTACAGGGGAAATGAAGGGACCCTGGAATCCATCAGTGAAAAGACTTTCTCATCTACTGTATTCATTGAAACTGGCCC
TTTCAAAAGACACAGAATGGAAGGAATCAAATATGAAGGCATTTCTAAACTTGCC

Alignment

ORF - retro_cpor_818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.9 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MGKSDFLTPKAIANRIKSKGLQKLRWYCQMCQKQCRDENGFKCHCMSESHQRQLLLASENPQQFMDYFSE
          .GKSDF..P..I.N.I..K..QKL.W.CQ..QKQC.DENGF...CMSE..Q.QLLLASE..QQ..D.FSE
Retrocopy IGKSDFVIPRTISNWIQCKVFQKLPWCCQI*QKQCQDENGFQDYCMSE*NQTQLLLASEHSQQWTDCFSE

Parental  EFRNDFLELLRRRFGTKRVHNNIVYNEYISHREH--IHMNATQWETLTDFTKWLGREGLCKVDETPK-GW
          ....D.LE.LRR.FGT..VHNN.V.N..I.H.EH.........WE.L.DFTKW.GR.GLCKVDETPK..W
Retrocopy KSHSD-LEILRR*FGTCQVHNNLVCNQFIRHQEHSVTYEHSAEWEMLMDFTKWQGRQGLCKVDETPK<DW

Parental  YIQYIDRDPETIRRQLELEKKKKQDLDDEEKTA-KFIEEQVRRGLEGKEQEA-PVFTELSREN-DEEKVT
          YIQYI..DPET...Q.EL.KKKKQ.LD.EEK.A.K.IE.QV..GL..K.QE..PVF.E...E..D..KVT
Retrocopy YIQYISWDPETSQWQMELGKKKKQNLDSEEKWA<KLIEKQVQQGLKRKDQEV<PVFMEFEEEK<DKVKVT

Parental  FNLNKGACSSSGATTSKSSSLGPSALKTLGSTASVKRKETSQSSAQSKEKKKKKSALDEIMEIEEEKKRT
          F.L..GA..S.G...SK.SSLGPS.LK.L...ASVK.KET.QSSA.S.EKKKK.S...EIME.EEE.KR.
Retrocopy FVLEQGAPISAGSSSSKTSSLGPSSLKMLRRMASVKQKETFQSSARSQEKKKK-SSIEEIMESEEERKRK

Parental  SRTDYWLQPEIIVKIITKKLGEKYHKKKGIVKEVIDRYTAVVKMIDSGDKLKLDQTHLETVIPAPGKRIL
          ..T.YWLQP.I.VKI.T..L....H.K.G...EVI..YTA.VK.IDS.D.LKL.Q..LET.....GK.I.
Retrocopy PHTEYWLQPKITVKIRTNNLAVNSHQKNGVDMEVINKYTAIVKLIDSRDQLKLYQSPLETGNAGQGKIIS

Parental  VLNGGYRGNEGTLESINEKTFSATIVIETGPLKGRRVEGIQYEDISKLA
          VLN..YRGNEGTLESI.EKTFS.T..IETGP.K..R.EGI.YE.ISKLA
Retrocopy VLNASYRGNEGTLESISEKTFSSTVFIETGPFKRHRMEGIKYEGISKLA

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_818 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_818 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.

---

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,