RetrogeneDB ID: retro_itri_487

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393295.1:8412075..8413262(+)
• 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_487
ATGACTGCTGGGCCGATATCTGAATGGAACTAGGATGCCACTGTGTACATGGGGTTAGTGATGAGGTTAGTGAACCACTG
CTCTGAGAACTCTTTCTCCAGGCAGGGCCCATGGTCAACACCCACATGCCAAAGGATAGAGTCACTGGCCAGCACCAAGG
TTATGGCTTTTTATGAATTCTTGAGTGAGGAAGATGCTGACTATGCCATTAAGATTATGAACATGATCCAACTCTATGGA
CAGCCAATATGTATAAACAAGGCATCTGCTCACAGCAAAAACCTGGATGTAGGGGCCAACATTTTCACTGGGAACCTGGA
CTCAGAAATTGATGAGAAGCTGCTTGATGATACTTTTAGTGTCTTTGGAGTCATCTTACAATCACCTAAAATTACGCGGG
ACCCTGATATAAGCAACTCCAAAGGTAATGCCTTTATTAATTTTGCTTCGTTGGATGCTTCGGATGCAGCAATTGAGGCC
ATGAATGGGCTGTACCTCTGTAGCCACCCTATCACTGTATCTTATGCGTTCAAGAAGGACTCTAAGGGCCAGCGTCATGG
CTCAGCAGCTGAACAACTTCTGGCAGCCAAGAACCCACTCTCCCAGGCTGACTGTCCTCATCAGCTGTTGGCAGATGCAC
CCTCTCCACCTTCTGCCCCCAATCCTGTGGCGTCATCATTGGGATCTGGGCTTCCTCCACCAGGCAAGCCTCCTCCTGGC
TCCTTCCAACTCTGGTGCCGCTTCCTGTAGCCCTCCCATTTGGGATACCTTCAGCCATGTCCCCACCACCTATGCTGCCT
GGGGCTGGAAGACATGGCCCTCCATCAGCAGGAACTCCAGAGGTTGGACATCCTGGTCATGGGCATTCTAATTCTCACCC
GTTCCCACAAGGTGGGATGCCCCATCCAGGAATGTCTCAGATGCAGCTGGCCCTCATGGCTTAGGACACCCACATGCTGT
GGACCTCCAGGCTCAGGGGGGCAACCACCACCCTCACCACCACCTGGAAGGCCTCATCCTGGACCTCCTCCACTGGGCAT
GCCCCCTGAGGACCTTTGTTTGGATCTCCAGTGGGTCACCCAGGTCCTATGCCTCCACATGGTATGTGTGGGCTTCCTCC
ACTGATGCCACCTCATGGATACACTGGTTCTCCACAACCCCGTCCCTGCACCCAGACCCATGCCCCA

Alignment

ORF - retro_itri_487 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.12 %
• Parental protein coverage: 94.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MAAGPISERNQDATVYVGGL-DEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFV-EFLSEEDAD
          M.AGPISE.N.DATVY.G...DE.VSEPLL.ELFLQAGP.VNTHMPKDRVTGQHQGYGF..EFLSEEDAD
Retrocopy MTAGPISEWN*DATVYMGLV<DE-VSEPLL*ELFLQAGPMVNTHMPKDRVTGQHQGYGFL>EFLSEEDAD

Parental  YAIKIMNMIKLYGKPIRVNKASAHNKNLDVGANIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDT
          YAIKIMNMI.LYG.PI..NKASAH.KNLDVGANIF.GNLD.EIDEKLL.DTFS.FGVILQ.PKI.RDPD.
Retrocopy YAIKIMNMIQLYGQPICINKASAHSKNLDVGANIFTGNLDSEIDEKLLDDTFSVFGVILQSPKITRDPDI

Parental  GNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVSYAFKKDSKGERHGSAAERLLAAQNPLSQADRPH
          .NSKG.AFINFAS.DASDAAIEAMNG.YLC..PITVSYAFKKDSKG.RHGSAAE.LLAA.NPLSQAD.PH
Retrocopy SNSKGNAFINFASLDASDAAIEAMNGLYLCSHPITVSYAFKKDSKGQRHGSAAEQLLAAKNPLSQADCPH

Parental  QLFADAPPPPSAPNPVVSSLGSGLPPPGMPPPGSF-PPPVPPPGALPPGIPPAMPPPPMPPGAGGHGPPS
          QL.ADAP.PPSAPNPV.SSLGSGLPPPG.PPPGSF.P..VP.P.ALP.GIP.AM.PPPM.PGAG.HGPPS
Retrocopy QLLADAPSPPSAPNPVASSLGSGLPPPGKPPPGSF<PTLVPLPVALPFGIPSAMSPPPMLPGAGRHGPPS

Parental  AGTPGAGHPGHGHSHPHPFPPGGMPHPGMSQMQLA-HHGPHGLGHPHAGP-PGSGGQPP-PRPPPGMPHP
          AGTP..GHPGHGHS..HPFP.GGMPHPGMSQMQLA..HG...LGHPHA...P...G..P.P.PPPG.PHP
Retrocopy AGTPEVGHPGHGHSNSHPFPQGGMPHPGMSQMQLA<PHG---LGHPHAVD<PPGSGGQPPPSPPPGRPHP

Parental  GPPPMGMPPR-GPPFGSPMGHPGPMPPHGMRGPPPLMPPHGYTGPPRPPPYGYQRGP
          GPPP.GMPP..GP.FGSP.GHPGPMPPHGM.G.PPLMPPHGYTG.P.P.P......P
Retrocopy GPPPLGMPPE<GPLFGSPVGHPGPMPPHGMCGLPPLMPPHGYTGSPQPRPCTQTHAP

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_487 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_487 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.

---

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,