RetrogeneDB ID: retro_cpor_761

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_263:236533..237552(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000003074
• Aliases: None
• Description: None

Sequence

>retro_cpor_761
TGTGAGCTCTGCACAGGGTCTATGCCCATGTACATTGGGGAGGTGTCTTCTACACCCTGTAGGGCAACTTTAGCACCCTC
CACCAGCTGGGCATCATCATCATCAGGATTCTGATGCTTCAGATCTTTGGCCTGCAATTAACATTGTGGACTGAAGAGTA
CTGGCCTCTCCTACTAGCCTTCACCATCATCCCAGCCTTCTTAGGAAGTGTAGTGCTCCTTTTCTGCCTGAAAGTCCTAG
ATTCTTCCTGATTAACAGAAAGGAGGAGAAGGTGTTATGAAGATTTTGCAGTGATTATGCGGCTCCCACGATGTGTCCTA
GAACATCCCGGAGATGAAGAATGAGAAATGAGATAGGAGGAGGAAGTCACCTTGCAGGAGCTCTTCAGATCCCAGAGATA
CCAGCAGGCCATCATCAATGTCACCATGCTGTAGGTCTCCCAGCAGCTCTTTGGGAATCAATGCTGCGTTCTATTATTCA
ACAAGAATCTTCAACAATGCAGGCATCCAGGGGCCAATCTATGCTAACATTGGAGCAGGGATGGTAAACACCATCTTAAC
TGTGTTTCTGGTGTACAGAGTGGTAAGGGGGAACCTGCATATGATCAGCTTCAGCAGCTTGGCTGTTTGTTCCATCACCA
TGACAATCTCTCTGTTACTGAAGGACACACACAGTTTCATGAGCTACATCTGCATCATGGCAGTCTTGACATACATGGCC
TTCCATGAGGTCAGACTAGGACCCATCTTCTGGTTCACTGTGGCCACCCTCTTCAGCCACGGATCCCTGTCTGGTAGCCA
TGTCCATGACTGGTTATTCTAACTGGACCACCAACTTTGTAGTTGGACTGCTTTACCCTTTGGCTGAAGACTCTGAATCC
CTACATTTTTATCACCTTCACCATCTTCCTTATTATCTGCCTGCTGTTCACCTTCTTCAAAGTTCCAGAGACCCAAGGCA
GAACGTTTGAAGACATAACCTGGGTCTATGAAGAGTTTGCTAGTGAGGCGCAAGGGCCT

Alignment

ORF - retro_cpor_761 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.15 %
• Parental protein coverage: 73.09 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  CGLCTGFVPMYIGEVSPISLR-GAFGTLHQLGIVI-GILVAQVFGLKFILGTEERWPVLLGGTILPAFLQ
          C.LCTG..PMYIGEVS....R.G.F.TLHQLGI.I..IL..Q.FGL...L.TEE.WP.LL..TI.PAFL.
Retrocopy CELCTGSMPMYIGEVSSTPCR<GNFSTLHQLGIIIIRILMLQIFGLQLTLWTEEYWPLLLAFTIIPAFLG

Parental  SVALPFC-PESPRFLLINRNEE-ERATKILQRLWGTQDVSQDIQEMKDE-SVQMNQEPTVTVLELFRSRK
          SV.L.FC.PESPRF.LINR.EE.E...KILQ.L.G..DVS..I.EMK.E.......E.T...L..FRS..
Retrocopy SVVLLFC<PESPRFFLINRKEE<EGVMKILQ*LCGSHDVS*NIPEMKNE<EMR*EEEVTLQEL--FRSQR

Parental  YQQPILIAIMLQLSQQL-SGINAVFYYSTGIFKDAGVQEPIYATIGAGVVNTIFTVFSVFLVESVGRRSL
          YQQ.I....ML..SQQL..GINA.FYYST.IF..AG.Q.PIYA.IGAG.VNTI.TVF...LV..V.R..L
Retrocopy YQQAIINVTML*VSQQL>LGINAAFYYSTRIFNNAGIQGPIYANIGAGMVNTILTVF---LVYRVVRGNL

Parental  HMTGLGGMAVCSIIMTVSLLLKSTYNFMSYICIAAILIYVAFFEIGPGPIPWFIVAELFSQG-PRPAAMA
          HM......AVCSI.MT.SLLLK.T..FMSYICI.A.L.Y.AF.E...GPI.WF.VA.LFS.G.P...AM.
Retrocopy HMISFSSLAVCSITMTISLLLKDTHSFMSYICIMAVLTYMAFHEVRLGPIFWFTVATLFSHG>PCLVAMS

Parental  VAGCSNWTSNFLVGLLFPLA--AASLGAY-VFLIFAVFLIIFLLFTFFKVPETRGRTFEEITRTFEGNTR
          ..G.SNWT.NF.VGLL.PLA....SL..Y..F.IF.....I.LLFTFFKVPET.GRTFE.IT...E....
Retrocopy MTGYSNWTTNFVVGLLYPLAEDSESLHFY>TFTIFLI---ICLLFTFFKVPETQGRTFEDITWVYEEFAS

Parental  VSGGP
          ...GP
Retrocopy EAQGP

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	0.12 RPM
SRP017611_kidney	0.00 RPM	0.10 RPM
SRP017611_liver	0.00 RPM	0.44 RPM
SRP040447_lung	0.00 RPM	6.83 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.21 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_761 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_761 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004556	2 retrocopies	retro_btau_708, retro_btau_709,
Callithrix jacchus	ENSCJAG00000018988	1 retrocopy	retro_cjac_446,
Cavia porcellus	ENSCPOG00000003074	1 retrocopy	retro_cpor_761 ,
Cavia porcellus	ENSCPOG00000009834	1 retrocopy	retro_cpor_760,
Cavia porcellus	ENSCPOG00000011295	1 retrocopy	retro_cpor_587,
Felis catus	ENSFCAG00000001625	1 retrocopy	retro_fcat_1924,
Homo sapiens	ENSG00000059804	2 retrocopies	retro_hsap_3983, retro_hsap_401,
Gorilla gorilla	ENSGGOG00000016813	1 retrocopy	retro_ggor_398,
Macaca mulatta	ENSMMUG00000000439	2 retrocopies	retro_mmul_2301, retro_mmul_502,
Nomascus leucogenys	ENSNLEG00000026903	2 retrocopies	retro_nleu_1572, retro_nleu_1904,
Oryctolagus cuniculus	ENSOCUG00000008575	1 retrocopy	retro_ocun_352,
Pongo abelii	ENSPPYG00000004234	1 retrocopy	retro_pabe_3274,
Pongo abelii	ENSPPYG00000004235	1 retrocopy	retro_pabe_315,
Pan troglodytes	ENSPTRG00000004624	1 retrocopy	retro_ptro_2703,
Pan troglodytes	ENSPTRG00000004626	1 retrocopy	retro_ptro_307,