RetrogeneDB ID: retro_itri_682

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393310.1:10406383..10406893(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3A
• Ensembl ID: ENSSTOG00000026363
• Aliases: None
• Description: 5'-nucleotidase, cytosolic IIIA [Source:HGNC Symbol;Acc:17820]

Sequence

>retro_itri_682
GGAGAGCCTGCTGTACTTATCAAAATGATGCCAGAGTTCCAGAAAAGTTCAGTTCGTATCAAGAACCCTGTAAGAGTAGA
AGAAACTCTCTGTGGTCTTATCAAAGGAGGAGTTGCCAAACGTCAGATAGTAACAGACATTGATATGACACTAAGTAGGT
TTCCTACACAGGGAAAAGATGCCCAACATGTCATAATATCATTGACAACTGTCAGCTGGTTACAGACAAATGTAAAATAA
TAAAAGTTATTGCAACTAAAGGAACAGCATTATGCTATAGAAGTTGATCCTGTTCTTACCGTGGAAGAAAAGTACCCTTA
AATGGTAGAATGGTATAGTAAGTCTCACGGTTTGATTGTGGAACAGGGTATACCAAAAGCTAAACTTAAAGAGATTGTGG
AAGTATCTGACGTTATGCTCAAGGAAGGATATGAGGATTTCTTTGTTAAGCTCCAACACAGTATCCCTGTGTTCATATTT
TAGGCTGGTATTGGTGAAGTTATCCATCAA

Alignment

ORF - retro_itri_682 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.88 %
• Parental protein coverage: 51.36 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GRKTKIIEMMPEFQKSSVRIKNPTRVEETLCGLIKGGAAKLQIITDFDMTLSRF-SYKGKRCPTSHNIID
          G.....I.MMPEFQKSSVRIKNP.RVEETLCGLIKGG.AK.QI.TD.DMTLSRF.SY.GKRCPT.HNIID
Retrocopy GEPAVLIKMMPEFQKSSVRIKNPVRVEETLCGLIKGGVAKRQIVTDIDMTLSRF<SYTGKRCPTCHNIID

Parental  NCKLVTDECR-KKLLQLK-EQYYAIEVNPGLTVEEKYPHMVEWYSKSHSLIVEQGIPKAKIKEIVEESDV
          NC.LVTD.C...K....K.EQ.YAIEV.P.LTVEEKYP.MVEWYSKSH.LIVEQGIPKAK.KEIVE.SDV
Retrocopy NCQLVTDKCKIIKVIATK>EQHYAIEVDPVLTVEEKYP*MVEWYSKSHGLIVEQGIPKAKLKEIVEVSDV

Parental  MLKEGYEDFFDKLKQYNIPVFIFSAGIGDVLEE
          MLKEGYEDFF.KL.Q..IPVFIF.AGIG.V...
Retrocopy MLKEGYEDFFVKL-QHSIPVFIF*AGIGEVIHQ

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_682 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_682 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006624	1 retrocopy	retro_amel_875,
Bos taurus	ENSBTAG00000016709	1 retrocopy	retro_btau_1465,
Canis familiaris	ENSCAFG00000003154	1 retrocopy	retro_cfam_1295,
Equus caballus	ENSECAG00000011777	1 retrocopy	retro_ecab_1118,
Homo sapiens	ENSG00000122643	1 retrocopy	retro_hsap_3084,
Gorilla gorilla	ENSGGOG00000028164	1 retrocopy	retro_ggor_2119,
Mustela putorius furo	ENSMPUG00000005546	2 retrocopies	retro_mputfur_1175, retro_mputfur_577,
Pteropus vampyrus	ENSPVAG00000013182	2 retrocopies	retro_pvam_148, retro_pvam_706,
Rattus norvegicus	ENSRNOG00000005981	1 retrocopy	retro_rnor_632,
Sus scrofa	ENSSSCG00000022912	1 retrocopy	retro_sscr_540,
Ictidomys tridecemlineatus	ENSSTOG00000026363	2 retrocopies	retro_itri_1325, retro_itri_682 ,