RetrogeneDB ID: retro_itri_1153

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393388.1:3499353..3500537(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3B4
• Ensembl ID: ENSSTOG00000000684
• Aliases: None
• Description: splicing factor 3b, subunit 4, 49kDa [Source:HGNC Symbol;Acc:10771]

Sequence

>retro_itri_1153
GAACCAAACCAGGATGCCACTGTGTACGTGGGGGGCCTAGGTGAGAAGGTTTGTGAACCACTTCTGTGGGAACTCTTTCT
CCAGGCAGGGCCCGTGGTCAACACCCACATGCCAAAATATAGAGCCGCTGGTCAGCACCAAGGTTATGGCTTTGTTGAAT
TCTTGAGTGAGGAAGATGCTGACTGTGCCATTAAGATCATGAACCTGATCAAACTCTATGGACAGCCAATATGTGTAAAC
AGGGCATCTGCTCACAACAAAAACCTGGATGTAGGGGCCAACATTTTCACTGGGAACCTGGACCCAGAGATTGATGAGAA
GCTGCTTTATAATACTTTCAGCGCCTTTGGGGTCATCTTACAAATACCTAAAATTATGTGGGACCCTGATACAGGCAACT
CCAAAGGTTAAGCCTTTATTAATTTTGCTTCGTTTGATGCTTCGGATGCAGCCATTGAGGCCATGAATGAGCAGTACCTC
TGTAACCGCCTTATCACTATATCTTACTTGTTCAAGAAGAACTCTAAGGGGGACCGCCATGTGTCAGCAGCTGAATGACT
TCTAGTAGCCCAGAACCCACTCTCCCAGTCTGACCGTCCTTATTAGCTATTCACAGATGCACCCCTTCCACTTCCACCCC
CAATCCTGGGGTGCCATCATTGGGGTCTTGGCTTCCTCCACCAGGCATGCCTCCTCCTATCTCCTTGCTACCTCCAGTGC
CGCCTCCTGGAGCCCTCTCACCTCCGGCCATGCCCCCACCACCTATGCCTCCTGGGGCTGGAGGACATAGCCCTCCATCA
TCAGGAACCACAGGGGCTGGACATCCTGGTCATGGACATTCTCACCCTCACCTGTTCCCACCAGGTGGGATGCCCCATCC
AGGAATGTCCCATATGCACCTGGCCTACATGGTCCTCATGGCTTAGGATACTCACATGCTAGACCTCCACGCTCTGGGGG
GCAACCACCACCCCGACCCCCACCTGGAATGCCTCATCCTGGACCTCCTCCAGTGGGCATGCCCCCACTGCCAGGATCTC
CACTTGGATCTCCCATGGGTCACCCAGGTCCTATGCCTCCTCTTGGTGTGCGTGGGCCTCCTCCACTGATACCACCTCAT
GGATACACTGGCCCTCACTATGGCTATCAATGGGGGCCCCCTCGCCATCCAGACGCCCCCACCT

Alignment

ORF - retro_itri_1153 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.55 %
• Parental protein coverage: 93.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ERNQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMNMI
          E.NQDATVYVGGL.EKV.EPLLWELFLQAGPVVNTHMPK.R..GQHQGYGFVEFLSEEDAD.AIKIMN.I
Retrocopy EPNQDATVYVGGLGEKVCEPLLWELFLQAGPVVNTHMPKYRAAGQHQGYGFVEFLSEEDADCAIKIMNLI

Parental  KLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFI
          KLYG.PI.VN.ASAHNKNLDVGANIF.GNLDPEIDEKLLY.TFSAFGVILQ.PKIM.DPDTGNSKG.AFI
Retrocopy KLYGQPICVNRASAHNKNLDVGANIFTGNLDPEIDEKLLYNTFSAFGVILQIPKIMWDPDTGNSKG*AFI

Parental  NFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPHQLFADAP-P
          NFASFDASDAAIEAMN.QYLCNR.IT.SY.FKK.SKG.RH.SAAE.LL.AQNPLSQ.DRP..LF.DAP.P
Retrocopy NFASFDASDAAIEAMNEQYLCNRLITISYLFKKNSKGDRHVSAAE*LLVAQNPLSQSDRPY*LFTDAP<P

Parental  PPSAPNPVVSSLGSGLPPPGMPPPGSFPPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPSAGTPGAGHP
          ..S.PNP.V.SLGS.LPPPGMPPP.S..PPVPPPGAL.P...PAMPPPPMPPGAGGH.PPS.GT.GAGHP
Retrocopy STSTPNPGVPSLGSWLPPPGMPPPISLLPPVPPPGALSP---PAMPPPPMPPGAGGHSPPSSGTTGAGHP

Parental  GHGHSHPHPFPPGGMPHPGMSQMQLAH-HGPHGLGHPHAGPPGSGGQPPPRPPPGMPHPGPPPMGMPP-R
          GHGHSHPH.FPPGGMPHPGMS.M.LA..HGPHGLG..HA.PP.SGGQPPPRPPPGMPHPGPPP.GMPP..
Retrocopy GHGHSHPHLFPPGGMPHPGMSHMHLAY<HGPHGLGYSHARPPRSGGQPPPRPPPGMPHPGPPPVGMPPLP

Parental  GPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGP-LPPP
          G.P.GSPMGHPGPMPP.G.RGPPPL.PPHGYTGP......G..R.P..PPP
Retrocopy GSPLGSPMGHPGPMPPLGVRGPPPLIPPHGYTGPHYGYQWGPPRHP>TPPP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_1153 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1153 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 16 parental genes, and 23 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,
Ictidomys tridecemlineatus	ENSSTOG00000012459	1 retrocopy	retro_itri_889,