RetrogeneDB ID: retro_itri_48

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393491.1:1822742..1823855(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000019472
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_itri_48
ATGGATGTAGAAGCCAAGTACCGCATGGCCTCCTTGTACGTGGGTGACCTGCACGTAGATGTCACCGAGGACCTATTGTT
CAGGAAGTTCAGTGCGGTGGGCCCTGTGCTGTCCATCCGCATCTGCAGGGACGCGGTCACCCGCCTCTCTCTGGGCTATG
CTTACGTGAACTTCCTGCAGTTGGCCGATGCCCAGAAGGCTCTAGACACCATGAACTTTGACACGATAAAAGGCAAATCC
ATCCGTCTCATGTGGTCTCAAAGGGATGCCCACCTAAGGAAATCTGGAGTTGGGAATGTGTTCATCAAAAACCTGGACAA
ATCCATAGATAACAAGACGCTGCACGAACATTTTTCAGCTTTTGGAAAGATCCTTTCCTCCAAGGTGATGAGTGATGACC
AAGGCTCCAAGGGTTACGGCTTCGTGCACTTTCAGAACCAGAGCGCGGCCGAGAAGGCCATCGAGGAGATGAACGGGAAG
CTGCTCAAAGACTGCAGGGTGTTTGTGGGCAGATTCAAAAACCGCAAGGAGCGCGAGGCCGAGCTCAGAAGCAAAGCCTC
CAGCGAATTCACCAACGTTTACATCAAAAACTTTGGGGATGACATGGATGATGAGAGACTGAAGGAGGTTTTCAGCAAGT
ATGGCCACCCCCTGAGTGTGAAGGTGATGAGAGACGCCAGCGGGAAATCCAAAGGCTTCGGCTTCGTGAGCTTCGAGAGC
CACCAGGCTGCCCAAAAGGCAGTTGAAGAAATGAACGGAAAGGACATAAACGGGCAGCCGGTTTTTGTGGGCAGGGCACA
AAAGAAAGGAGAGAGGCAGGCTGAGCTAAAGGAAATGTTTGAGCAGAAGAAAAAGGAAAGAATCCGTGGACGCCAGGGGG
TAAAACTGTACATTAAGAATCTGGACGATTCCATCGATGATGAGAAGCTACGGAAGGAGTTTTCTTCTTTTGGATCCATT
AACAGAGTGAAGGTAATGCAGGAGGAAGGGCAGAGCAAGGGGTTCGGCCTCATCTGCTTCTCCTCCTCCGAGGAGGCCCT
CGCAGCCATGGCTGAGATGAATGGCCGCATCTTGGGCTCCAAAGCCCTGAACATTGCCCTGGCCCAGAAGCAT

Alignment

ORF - retro_itri_48 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 59.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVI
          Y.MASLYVGDLH.DVTE..L..KFS..GP.LSIR.CRD..TR.SLGYAYVNF.Q.ADA..ALDTMNFD.I
Retrocopy YRMASLYVGDLHVDVTEDLLFRKFSAVGPVLSIRICRDAVTRLSLGYAYVNFLQLADAQKALDTMNFDTI

Parental  KGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFET
          KGK..R.MWSQRD..LRKSGVGN.FIKNLDKSIDNK.L...FSAFG.ILS.KV..D..GSKGYGFVHF..
Retrocopy KGKSIRLMWSQRDAHLRKSGVGNVFIKNLDKSIDNKTLHEHFSAFGKILSSKVMSDDQGSKGYGFVHFQN

Parental  QEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARA-KEFTNVYIKNFGEDMDDERLKDLFGKFGP
          Q.AAE.AIE.MNG.LL.D..VFVGRFK.RKEREAEL...A..EFTNVYIKNFG.DMDDERLK..F.K.G.
Retrocopy QSAAEKAIEEMNGKLLKDCRVFVGRFKNRKEREAELRSKASSEFTNVYIKNFGDDMDDERLKEVFSKYGH

Parental  ALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKFEQMKQD
          .LSVKVM.D.SGKSKGFGFVSFE.H..AQKAV.EMNGK..NG....VGRAQKK.ERQ.ELK..FEQ.K..
Retrocopy PLSVKVMRDASGKSKGFGFVSFESHQAAQKAVEEMNGKDINGQPVFVGRAQKKGERQAELKEMFEQKKKE

Parental  RITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGR
          RI...QGV.LY.KNLDD.IDDE.LRKEFS.FG.I...KVM.E.G.SKGFG..CFSS.EEA..A..EMNGR
Retrocopy RIRGRQGVKLYIKNLDDSIDDEKLRKEFSSFGSINRVKVMQEEGQSKGFGLICFSSSEEALAAMAEMNGR

Parental  IVATKPLYVALAQR
          I...K.L..ALAQ.
Retrocopy ILGSKALNIALAQK

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_48 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_48 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 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 ,