RetrogeneDB ID: retro_itri_485

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393294.1:18672542..18673380(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A3
• Ensembl ID: ENSSTOG00000027633
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 [Source:HGNC Symbol;Acc:10989]

Sequence

>retro_itri_485
CTGGTACACATGGCATGGGAAAACCCTTCAACATGCCACACCTGCAGCTGGTGCATGATGGCCTCTTGGGACCCAGTAGC
AGCCTCACCAGGACCCTGTGCCCACCCCAACATCTTGGCAAGCTGGCAGCCTGCTGTAGAAGAGAACAGCTGTTACTGTG
GCTCCATGGAGTTTTATGCACATGGGGCTTTGGTGGGGTCTTAAGTTGTGGGCTGACACACATGGCTGTTCCCCTGTATT
TAGTGAAATGCTGTATGCAGGTGAACCCCCAAAAGCACCAGATGCATTGAATGGATTCTCCTTATACTTAAGGAGGATGG
TGTTCTGATTAAAGGATGGGTCCAGCTTTCACTGGCTCCTCTAGCCAGGGCTTTGCAGCTTGGCTTTCATGAAGTTTTCA
AAGCCTTGGATAGAAACTGCATGGGGAGGAGAATGCCTATCTCTGGTGCACATCACTATGTTTGGCTGTCTCTGCCAGAG
CTGAGTTCTTTGCTGACATTGCCCTGGCTCCTAAAGAAACTGCTGAAGATCAGATTCAAACTCAACCAGGCTATGCCAAC
ACTTGGAGGGATGCAGTTCCCAAAATGTATATGGAAGAAGGCAAAAAAGCATTGCTCCCAGGAGGGCTCCTCTCTGTGTG
GGACAGACACTGTGCACCGAGATGAAGGCCACCTGCGCTGAGTGTGCTGTTGAAGCGTCACTCAGGTCTGTGGTTTCTAA
GCCCACCAGCGAGTACACAAAAGCAGTGCAGCTGGTTGGGACATATGTGGCAAGTGACACAGCTAGAGTCTTCTTTGCAA
CTGACCCTTAACCTGCTGATTCTGGAGTGTCCGTGCTC

Alignment

ORF - retro_itri_485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.93 %
• Parental protein coverage: 79.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 10

Retrocopy - Parental Gene Alignment:

Parental  VVHLARANP-FNAPHLQLVHDGLSGPSSSPTGPPGPPRRSRNLAAA-AVEEQYSCDYGSGRFFI-LCGLG
          .VH.A..NP.FN.PHLQLVHDGL.GPSSS.T....PP.....L.AA.AVEE..SC..GS..F.....G.G
Retrocopy LVHMAWENP<FNMPHLQLVHDGLLGPSSSLTRTLCPPQHLGKL-AA>AVEEN-SCYCGSMEFYA<TWGFG

Parental  GIISCGTTHTALVPLDLVKCRMQVDPQKYK-GIFNGFSV-TLKEDGVRGLAKGWA-PTFIGYSMQG-LC-
          G..SCG.TH.A.VPL.LVKC.MQV.PQK......NGFS...LKEDGV..L.KGW..P.F.G.S.QG.LC.
Retrocopy GVLSCGLTHMA-VPLYLVKCCMQVNPQKHQ<DALNGFSL<ILKEDGV--LIKGWV<PAFTGSSSQG<LC<

Parental  KFGFYEVFKVLYSNMLG-EENAYLWRTSLYLAASASAEFFADIALAPMEATKVRIQTQPGYANTLRDAAP
          ..GF.EVFK.L..N..G.EENAYLW.TSL.LA.SA.AEFFADIALAP.E.....IQTQPGYANT.RDA.P
Retrocopy QLGFHEVFKALDRNCMG<EENAYLWCTSLCLAVSARAEFFADIALAPKETAEDQIQTQPGYANTWRDAVP

Parental  KMYKEEGLKAFYKG-VAPLWMRQIPYTMMKFACFERTVEALYKFVVPKPRSECTKAEQLVVTFVAGYIAG
          KMY.EEG.KA...G..APL...Q...T.MK..C.E..VEA....VV.KP.SE.TKA.QLV.T.VA...A.
Retrocopy KMYMEEGKKALLPG<RAPLCVGQTLCTEMKATCAECAVEASLRSVVSKPTSEYTKAVQLVGTYVASDTAR

Parental  VFCAIVSHPADSVVSVL
          VF.A....PADS.VSVL
Retrocopy VFFATDP*PADSGVSVL

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_485 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_485 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 27 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013232	1 retrocopy	retro_acar_35,
Bos taurus	ENSBTAG00000012890	1 retrocopy	retro_btau_172,
Canis familiaris	ENSCAFG00000006545	1 retrocopy	retro_cfam_880,
Callithrix jacchus	ENSCJAG00000002392	2 retrocopies	retro_cjac_3315, retro_cjac_812,
Dipodomys ordii	ENSDORG00000011431	1 retrocopy	retro_dord_321,
Equus caballus	ENSECAG00000015135	1 retrocopy	retro_ecab_481,
Echinops telfairi	ENSETEG00000012678	1 retrocopy	retro_etel_1748,
Homo sapiens	ENSG00000075415	1 retrocopy	retro_hsap_392,
Gorilla gorilla	ENSGGOG00000015886	1 retrocopy	retro_ggor_394,
Latimeria chalumnae	ENSLACG00000007024	1 retrocopy	retro_lcha_4,
Macropus eugenii	ENSMEUG00000016593	2 retrocopies	retro_meug_405, retro_meug_658,
Microcebus murinus	ENSMICG00000003520	1 retrocopy	retro_mmur_298,
Myotis lucifugus	ENSMLUG00000008330	1 retrocopy	retro_mluc_1184,
Macaca mulatta	ENSMMUG00000023036	1 retrocopy	retro_mmul_496,
Monodelphis domestica	ENSMODG00000007717	2 retrocopies	retro_mdom_2026, retro_mdom_293,
Mus musculus	ENSMUSG00000061904	1 retrocopy	retro_mmus_1959,
Nomascus leucogenys	ENSNLEG00000005973	1 retrocopy	retro_nleu_2402,
Oryctolagus cuniculus	ENSOCUG00000011847	1 retrocopy	retro_ocun_390,
Otolemur garnettii	ENSOGAG00000012222	2 retrocopies	retro_ogar_1816, retro_ogar_2052,
Pongo abelii	ENSPPYG00000004858	1 retrocopy	retro_pabe_1768,
Pan troglodytes	ENSPTRG00000005333	1 retrocopy	retro_ptro_302,
Pteropus vampyrus	ENSPVAG00000005890	1 retrocopy	retro_pvam_212,
Sorex araneus	ENSSARG00000001149	1 retrocopy	retro_sara_262,
Ictidomys tridecemlineatus	ENSSTOG00000027633	2 retrocopies	retro_itri_485 , retro_itri_90,
Tupaia belangeri	ENSTBEG00000014548	1 retrocopy	retro_tbel_1792,
Tursiops truncatus	ENSTTRG00000004739	1 retrocopy	retro_ttru_692,
Vicugna pacos	ENSVPAG00000004704	1 retrocopy	retro_vpac_455,