RetrogeneDB ID: retro_itri_607

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393305.1:10786542..10787066(-)
• Located in intron of: ENSSTOG00000001573

Retrocopy information

• Ensembl ID: ENSSTOG00000024779
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SRI
• Ensembl ID: ENSSTOG00000004372
• Aliases: None
• Description: sorcin [Source:HGNC Symbol;Acc:11292]

Sequence

>retro_itri_607
GGAGAGACTCCTGGAGGACAAACGCAGAATCCTCTGTGTGGTCACTTTGCTGCTGTAGCAGGACAGGATGAGCAAATAGA
TGCTGCTGAATTGCAGAGACGTCTGCCACAGTTGGGCATTGCTGGAGGATACAAACCTTTTAACCTGGTGACTTGTCAGC
TTGCAATTTCAATGGTGGATAGAGACAGGTTTGGCATGATGGGCTTCAATGAATTTAAAGAACTCTGGGCTGCATTGAAT
GGCTGGAGACAACACTTCATCAGTTTTGATGGTGGTAGGAGTAGAACCTGGGATCCTCAAGAATTGCAGAAGGTGCTAAG
GACAACAGGCGCTGAGGCCGACTCCCCAAACTGAGTTCAATTGCAAAACAATACAGCACCAGTGGAAAGATCACCTTAGA
CGACTACATGGCCTGCTGTGTTGAGCTGAGGGCTCTCACAGAGAGCTTTTGAAGAGGGGACGCTGGGCAGCAAGGTGTTG
TGATTTTCCTTTAGGATGATTTCATTTAGTGTTTCCTGATTGTC

Alignment

ORF - retro_itri_607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.32 %
• Parental protein coverage: 88.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GPTFPGQTQDPLYGYFAAVAGQDGQIDADELQRCLTQSGIAGGYKPFNLETCRLMVSMLDRDRSGTMGFN
          G.T..GQTQ.PL.G.FAAVAGQD.QIDA.ELQR.L.Q.GIAGGYKPFNL.TC.L..SM.DRDR.G.MGFN
Retrocopy GETPGGQTQNPLCGHFAAVAGQDEQIDAAELQRRLPQLGIAGGYKPFNLVTCQLAISMVDRDRFGMMGFN

Parental  EFKELWSVLNGWRQHFISFDSDRSGTVDPQELQKALTTMGFRLNPQT-VNSIAKRYSTSGKITFDDYIAC
          EFKELW..LNGWRQHFISFD..RS.T.DPQELQK.L.T.G..........SIAK.YSTSGKIT.DDY.AC
Retrocopy EFKELWAALNGWRQHFISFDGGRSRTWDPQELQKVLRTTGAEADSPN<LSSIAKQYSTSGKITLDDYMAC

Parental  CVKLRALTDNFRRRDTGQQGMVNFSYDDFIQCVMTV
          CV.LRALT..F.R.D.GQQG.V.F..DDFI.C...V
Retrocopy CVELRALTESF*RGDAGQQGVVIFL*DDFI*CFLIV

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_607 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_607 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498,
Cavia porcellus	ENSCPOG00000010096	1 retrocopy	retro_cpor_216,
Latimeria chalumnae	ENSLACG00000000210	1 retrocopy	retro_lcha_89,
Loxodonta africana	ENSLAFG00000027380	2 retrocopies	retro_lafr_1186, retro_lafr_487,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782,
Mustela putorius furo	ENSMPUG00000018313	1 retrocopy	retro_mputfur_1147,
Pteropus vampyrus	ENSPVAG00000007438	2 retrocopies	retro_pvam_1112, retro_pvam_734,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,
Ictidomys tridecemlineatus	ENSSTOG00000004372	1 retrocopy	retro_itri_607 ,
Tupaia belangeri	ENSTBEG00000004434	1 retrocopy	retro_tbel_4493,
Tarsius syrichta	ENSTSYG00000014640	1 retrocopy	retro_tsyr_1832,
Xenopus tropicalis	ENSXETG00000008793	1 retrocopy	retro_xtro_25,