RetrogeneDB ID: retro_itri_139

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393459.1:2196835..2197984(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000022006
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000016395
• Aliases: None
• Description: None

Sequence

>retro_itri_139
ATGGGGAGCGGGGAGCCTAATCCTGCTGGCAAGAAAAAGAAGTACCTCAAGGCCGCCCTGTACGTGGGTGATTTGGACCC
TGATGTCACTGAGGACATGCTCTATAAGAAGTTCAGGCCCGCTGGCCCTCTGCGTTTCACCCGAATCTGCCGTGACCCAG
TGACCCGCAGCCCCCTGGGCTATGGCTATGTTAACTTCCGCTTTCCAGCGGATGCTGAATGGGCCCTGAACACCATGAAT
TTTGATTTGATTAATGGCAAACCATTCCGCCTCATGTGGTCACAGCCAGATGACCGCTTAAGAAAGTCTGGTGTTGGAAA
TATATTCATCAAAAACCTGGATAAATCAATTGACAATAGGGCCCTGTTCTATTTGTTTTCAGCTTTTGGGAACATTCTCT
CCTGCAAAGTTGTATGTGATGACAATGGCTCTAAGGGTTATGCCTATGTGCATTTTGACAGCCTGGCCGCTGCCAATAGG
GCCATCTGGCACATGAATGGAGTTCGGCTGAACAATCGCCAGGTATACGTTGGTAGATTCAAATTCCCAGAAGAGCGTGC
AGCTGAAGTCAGAACCAGGGATAGAGCAACATTCACTAATGTTTTTGTTAAAAACTTTGGAGATGACATGGATGACGAAA
AACTGAAGGAACTTTTCAGTGAATATGGGCCAACTGAGAGTGTAAAGGTAATAAGAGATGCCAGTGGGAAATCTAAAGGC
TTTGGGTTTGTAAGGTATGAGACACACGAGGCTGCCCAAAAGGCTGTGCTAGACCTGCATGGAAAGTCAATTGATGGGAA
AGTCCTGTATGTAGGGCGAGCACAGAAGAAAATTGAACGCCTAGCTGAGTTAAGGCGGAGATTTGAACGGCTAAGATTAA
AAGAAAAAAGTCGACCTCCGGGGGTGCCTATCTATATTAAAAACCTGGATGAGACCATCGATGATGAAAAACTGAAGGAG
GAATTTTCTTCATTTGGATCAATTAGCAGAGCCAAAGTGATGATGGAAGTAGGGCAAGGCAAAGGTTTTGGTGTTGTTTG
CTTTTCTTCTTTTGAAGAGGCTACCAAAGCAGTGGATGAGATGAATGGTCGAGTAGTGGGCTCCAAGCCCCTGCATGTCA
CCCTGGGCCAGGCCAGGCGCAGGTGGTGA

Alignment

ORF - retro_itri_139 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.75 %
• Parental protein coverage: 59.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
          Y..A.LYVGDL.PDVTE.MLY.KF.PAGP....R.CRD..TR..LGY.YVNF..PADAE.AL.TMNFD.I
Retrocopy YLKAALYVGDLDPDVTEDMLYKKFRPAGPLRFTRICRDPVTRSPLGYGYVNFRFPADAEWALNTMNFDLI

Parental  KGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFET
          .GKP.R.MWSQ.D..LRKSGVGNIFIKNLDKSIDN.AL...FSAFGNILSCKVVCD.NGSKGY..VHF..
Retrocopy NGKPFRLMWSQPDDRLRKSGVGNIFIKNLDKSIDNRALFYLFSAFGNILSCKVVCDDNGSKGYAYVHFDS

Parental  QEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAK-EFTNVYIKNFGEDMDDERLKDLFGKFGP
          ..AA.RAI..MNG..LN.R.V.VGRFK...ER.AE...R....FTNV..KNFG.DMDDE.LK.LF...GP
Retrocopy LAAANRAIWHMNGVRLNNRQVYVGRFKFPEERAAEVRTRDRATFTNVFVKNFGDDMDDEKLKELFSEYGP

Parental  ALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQD
          ..SVKV..D.SGKSKGFGFV..E.HE.AQKAV....GK...GK..YVGRAQKK.ER..EL.R.FE.....
Retrocopy TESVKVIRDASGKSKGFGFVRYETHEAAQKAVLDLHGKSIDGKVLYVGRAQKKIERLAELRRRFERLRLK

Parental  RITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGR
          ...R..GV..Y.KNLD..IDDE.L..EFS.FG.I..AKVMME.G..KGFG.VCFSS.EEATKAV.EMNGR
Retrocopy EKSRPPGVPIYIKNLDETIDDEKLKEEFSSFGSISRAKVMMEVGQGKGFGVVCFSSFEEATKAVDEMNGR

Parental  IVATKPLYVALAQRK
          .V..KPL.V.L.Q..
Retrocopy VVGSKPLHVTLGQAR

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_139 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_139 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 10 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Ictidomys tridecemlineatus	ENSSTOG00000016395	2 retrocopies	retro_itri_139 , retro_itri_48,