RetrogeneDB ID: retro_cpor_279

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_116:3465424..3466137(+)
• 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_279
AGGAGATGCTTTGGCACCAAGTGAGTCCATAACAATACAGTTTATGATGAACACAGCAGGAACTGAGAGCACATCCATAG
GAACGCTACTCAGTGGAAAACACTGATGGAATTATACTAAGTGGCTGGGAAGACACGGCCTGTGCCAAAGTGCATGAGGT
CCTCTAAGGCTGGTGTATCCAGCACACTACTGGGGACCCAGAGACTACTCACTGGCAGCTAGGGCGAGGGAAGCAGCATC
AGTATCTTGGCAATAAAGAGTAACCTGCCAAATTTATTGAAGAGCAAGTGCAAAGAGGTCTGAAAAGGAGGAGGAGGAGG
CCCCTGTCTTTATGGAATTCAGCAAAAGAATGATGAAAAAGTCACATTTCACATAAATCAAGGAATACCTAATTTCACCA
GGACCCACATCATACAAATCCTGTTCTTTGGGGCTAAGTGCATGGAAGATGCTTGGGAGAATTGCATCAGTGAAACCAAT
TTCCCAGAGCTCAGCCCAGTCTCAAAAGAAAAAGAAATCCACACTTGTGGAAATCATGGAGATTGAAGAGGAAAAGAACT
CAGATTCTTTGCTACAGCCTGAAATCACTGAAAATTAGAACCAAAAATCTTGCCGAGAAATACCTTCAAAAAACCAGTGT
GCTTAAGGAGGTCATTGACAAATACACAGCCATTATCAAAATGATCGATTCTGGAGACCAGCTGAAGCTTGAA

Alignment

ORF - retro_cpor_279 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.65 %
• Parental protein coverage: 63.1 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RRRFGTKRVHNNIVYNEYISHREHIHMNATQWETLTD-FTKWLGREGLC-KVDETPKGWYIQYIDRDPET
          RR.FGTK.VHNN.VY.E.....EHIH.NATQW.TL....TKWLGR.GLC.KV.E...GW.IQ....DPET
Retrocopy RRCFGTK*VHNNTVYDEHSRN*EHIHRNATQWKTLME>YTKWLGRHGLC>KVHEVL*GWCIQHTTGDPET

Parental  IRRQLELEKKKKQDLDDEEKTAKFIEEQVRRGL-EGKEQEAPVFTELSR-ENDEEKVTFNLNKGACS-SS
          ...QL....K..Q.L...E..AKFIEEQV.RGL.E..E.EAPVF.E.S...ND.EKVTF..N.G....S.
Retrocopy THWQLG-RGKQHQYLGNKE*PAKFIEEQVQRGL<EKEEEEAPVFMEFSK<KND-EKVTFHINQGIPN>SP

Parental  GATTSKSSSLGPSALKTLGSTASVKRKETSQSSAQSKEKKKKKSALDEIMEIEEEKKRTSRTDYWLQPEI
          G.T..KS.SLG.SA.K.LG..ASV..K..SQSSAQS...KKKKS.L.EIMEIEEEK......D..LQPEI
Retrocopy GPTSYKSCSLGLSAWKMLGRIASV--KPISQSSAQS--QKKKKSTLVEIMEIEEEK----NSDSLLQPEI

Parental  IV-KIITKKLGEKYHKK-KGIVKEVIDRYTAVVKMIDSGDKLKLD
          ...K...K.L.....KK.....KEVID.YTA..KMIDSGD.LKL.
Retrocopy TE<KLEPKILPRNTFKK<TSVLKEVIDKYTAIIKMIDSGDQLKLE

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	0.04 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_279 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_279 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,