RetrogeneDB ID: retro_cpor_234

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_105:3909717..3910850(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSCPOG00000008267
• Aliases: None
• Description: None

Sequence

>retro_cpor_234
CTTGGCGAGAGGGTTAGTGAGCTACTGCTGTGGAAACTCTTTCCCCAGGCTAGGCCAGTAGTCAATTCCTATATGCCAAA
GGACAGAGTCACTGGCCAGCTGCAAGGCTAAGGCTTTGTTGAATTCTTAAGTGAAGAAGATGCTGTCTATGCCATTAAGA
TTATGAACATGATCAAAATCTATAGGAAGCCAATAACAGTGAACAAAGTATCAGCTCACACCAAAAGCCTAGATATAAGG
GTCAACGTTTTCATTGGTAATCTGGACCCAGAAATTGATGAGAAATTGCTTTAGGATACTTTCGGTATCTTTGGGGTCAT
TTGAGAAATACCCAAAATTATGAGGGATGCTGACACAGGCAACTCCAAAGGTTATACATTTGTTCATTTTGCTTCATTTG
ATGCTTCAGATGCAGCCATTTAGACCATGAATGGGCCCTATCTCTATAATCACAGTATCACTATGGATAATGCCTTAAAG
AAGGACTCTAAGTTTGAGTACCATGGCTCAGCCACTGAACAACTTCCAGCAGCACAAAACCTGATCTCTCAGGCTGACCA
CCCTCATCAGCTGTTCACCAGAGCACACCCCCCACCCACTGCCCCCAATCCTGTGGCATCATCATTGGGATCTGGGCTTC
CTCCACCAGGCATGCTGCCTCCTGGCTCCTTCCCACCACCAGTGCCACCTCCCTGAGCTCTCCCATCTGGAATACCACTG
GCCATGCCACCACCACCTATGTGTCCTGGGGCTGGAGGACATGTTACCCTGTCAGCAGGAACCTCAGGGACCAGATATCC
TTGGTCTTGGACATTCACATCATCGCACTTTTGCACCAGCTGAGATGCCCCATCCAAGGGTCTCTCAGATGCAGCCAGAC
CAACATGATGCCCATGGCTTAGGACATTCCAGTGCTGGACCTCTAGGTCTGGGGATGGCCACCACCCCAGCTGCTACCAG
GGATGCCTCACCCTGGACTGTCTCTCCAAGGACATGCCACCCCCATGGCTCCATTTGGATCTCCCATGAGTCCCATGCTA
CCACTAGATATGTGTGTGTCTCCTCTAATGATGCCCCCTCGTGGGTACCGTGGGCCTCCATGACCACCTCCCTATGGCTC
CAGCAGGGCCCCT

Alignment

ORF - retro_cpor_234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.53 %
• Parental protein coverage: 89.86 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMNMIKLYGKPIRVNKA
          L.E.VSE.LLW.LF.QA.PVVN..MPKDRVTGQ.QG.GFVEFLSEEDA.YAIKIMNMIK.Y.KPI.VNK.
Retrocopy LGERVSELLLWKLFPQARPVVNSYMPKDRVTGQLQG*GFVEFLSEEDAVYAIKIMNMIKIYRKPITVNKV

Parental  SAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI
          SAH.K.LD...N.FIGNLDPEIDEKLL.DTF..FGVI...PKIMRD.DTGNSKGY.F..FASFDASDAAI
Retrocopy SAHTKSLDIRVNVFIGNLDPEIDEKLL*DTFGIFGVI*EIPKIMRDADTGNSKGYTFVHFASFDASDAAI

Parental  EAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQLFADAPPPPSAPNPVVSSLG
          ..MNG.YL.N..IT...A.KKDSK.E.HGSA.E.L.AAQN..SQAD.PHQLF..A.PPP.APNPV.SSLG
Retrocopy *TMNGPYLYNHSITMDNALKKDSKFEYHGSATEQLPAAQNLISQADHPHQLFTRAHPPPTAPNPVASSLG

Parental  SGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAGTPGAGHP-GHGHSHPHPFPP
          SGLPPPGM.PPGSFPPPVPPP.ALP.GIP.AMPPPPM.PGAGGH...SAGT.G...P.G.GHSH...F.P
Retrocopy SGLPPPGMLPPGSFPPPVPPP*ALPSGIPLAMPPPPMCPGAGGHVTLSAGTSGTRYP>GLGHSHHRTFAP

Parental  AGMPHPGMSQMQLAHHGPHGLGHPHAGPPG-SG-GQPPPRPPPGMPHPGPPPMGMPPRGPPFGSPMGHPG
          A.MPHP..SQMQ...H..HGLGH..AGP.G.SG.G.PPP...PGMPHPG....G......PFGSPM....
Retrocopy AEMPHPRVSQMQPDQHDAHGLGHSSAGPLG<SG<GWPPPQLLPGMPHPGLSLQGHATPMAPFGSPM---S

Parental  PMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGP
          PM.P..M...P..MPP.GY.GPP.PPPYG..R.P
Retrocopy PMLPLDMCVSPLMMPPRGYRGPP*PPPYGSSRAP

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	16.85 RPM
SRP017611_kidney	0.00 RPM	27.74 RPM
SRP017611_liver	0.00 RPM	14.71 RPM
SRP040447_lung	0.00 RPM	35.59 RPM
SRP040447_skeletal_muscle	0.00 RPM	9.87 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_234 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_234 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012495	2 retrocopies	retro_btau_1385, retro_btau_592,
Canis familiaris	ENSCAFG00000011617	3 retrocopies	retro_cfam_585, retro_cfam_711, retro_cfam_729,
Callithrix jacchus	ENSCJAG00000000793	3 retrocopies	retro_cjac_1297, retro_cjac_1909, retro_cjac_638,
Cavia porcellus	ENSCPOG00000008267	1 retrocopy	retro_cpor_234 ,
Echinops telfairi	ENSETEG00000008963	1 retrocopy	retro_etel_1310,
Homo sapiens	ENSG00000143368	1 retrocopy	retro_hsap_1356,
Gorilla gorilla	ENSGGOG00000004761	1 retrocopy	retro_ggor_1056,
Macaca mulatta	ENSMMUG00000007256	1 retrocopy	retro_mmul_2191,
Mustela putorius furo	ENSMPUG00000005563	2 retrocopies	retro_mputfur_1105, retro_mputfur_648,
Oryctolagus cuniculus	ENSOCUG00000004614	1 retrocopy	retro_ocun_1239,
Pongo abelii	ENSPPYG00000000912	1 retrocopy	retro_pabe_1124,
Pan troglodytes	ENSPTRG00000001243	1 retrocopy	retro_ptro_930,
Pteropus vampyrus	ENSPVAG00000014171	1 retrocopy	retro_pvam_931,
Rattus norvegicus	ENSRNOG00000021181	1 retrocopy	retro_rnor_2350,
Ictidomys tridecemlineatus	ENSSTOG00000000684	2 retrocopies	retro_itri_1153, retro_itri_487,