RetrogeneDB ID: retro_cpor_989

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_38:5133230..5133993(-)
• 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_989
ATTGGGAAGTCAGGCTTTCTTACTCCCAAGGCCATTGCCCACCGGATTCCATCTAAAGGGCTTCAAAAGTTGCGCTGGTA
TTGCCAGATGTGTGAGAAGCAATTCCGCATGAAAATGGCATTAAGTGTCACTGTATGTCAGAATCTCATCAGAGACAATT
ATTGCTGGCTTCAGAAAATCCTCAGCAGTTGATGGATTATTTTTCAGAGGAATTCCGCAGTGAGTTCTTAGAACTTCTCA
AGAGACGCTTTGGCACCAGGCGAGTCCATAGCAATATTGTCTACAGTGGGTACGTCAGCCCCGAGACCACAGGCACATGT
GTGCTGCTCAGTGGGAAACGCTGATGGATTTTACCAAGAGGCTGGGCAGACAAGGCCAGTGCAAGGTGGATCAGACCCCA
AGAGTGGTGCATCAGTACATCGACAGGGACCCAGAGACCATTCGCCTGCAGCTGGAGCTGGGCAAGAAGAAGAAGCAGGA
CCTTTAGGATGAAGAAAAGACTGCCACATTGATTGCAGAACAGATGCCAAGAGGTCTGCAAAGGAAGGAGCAGGAGGCCC
CTGTGTGTCTGGAATTAAGCAGAGAAAGCCATGAAGAGAAAGTTACACTTCATGTGAATCAAGGAACAGGTGTTTCAGCA
GGAGCAACGGCCTCCTGATCCAGTTGTTTGGGGCCCAGCACACTGATGATGCTGGGGAGAATGGCCTCAGTGAAAGGAAA
AGAAACTTCTCAGAGATTGGCTCAGGCTAAGGAAAGGAAAAGG

Alignment

ORF - retro_cpor_989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.87 %
• Parental protein coverage: 65.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGKSDFLTPKAIANRIKSKGLQKLRWYCQMCQKQCR-DENGFKCHCMSESHQRQLLLASENPQQFMDYFS
          .GKS.FLTPKAIA.RI.SKGLQKLRWYCQMC.KQ.R..ENG.KCHCMSESHQRQLLLASENPQQ.MDYFS
Retrocopy IGKSGFLTPKAIAHRIPSKGLQKLRWYCQMCEKQFR<HENGIKCHCMSESHQRQLLLASENPQQLMDYFS

Parental  EEFRNDFLELLRRRFGTKRVHNNIVYNEYISH-REHIHMNATQWETLTDFTKWLGREGLCKVDETPKGWY
          EEFR..FLELL.RRFGT.RVH.NIVY..Y.S..R.H.HM.A.QWETL.DFTK.LGR.G.CKVD.TP....
Retrocopy EEFRSEFLELLKRRFGTRRVHSNIVYSGYVSP<RDHRHMCAAQWETLMDFTKRLGRQGQCKVDQTPRVVH

Parental  IQYIDRDPETIRRQLELEKKKKQDLDDEEKTAKFIEEQVRRGLEGKEQEAPVFTELSRENDEEKVTFNLN
          .QYIDRDPETIR.QLEL.KKKKQDL.DEEKTA..I.EQ..RGL..KEQEAPV..ELSRE..EEKVT...N
Retrocopy -QYIDRDPETIRLQLELGKKKKQDL*DEEKTATLIAEQMPRGLQRKEQEAPVCLELSRESHEEKVTLHVN

Parental  KGACSSSGATTSKSSSLGPSALKTLGSTASVKRKETSQSSAQSKEKKK
          .G...S.GAT.S.SS.LGPS.L..LG..ASVK.KETSQ..AQ.KE.K.
Retrocopy QGTGVSAGATAS*SSCLGPSTLMMLGRMASVKGKETSQRLAQAKERKR

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_989 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_989 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,