RetrogeneDB ID: retro_itri_930

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393345.1:2804890..2806017(-)
• Located in intron of: ENSSTOG00000002689

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAPK4
• Ensembl ID: ENSSTOG00000022822
• Aliases: None
• Description: mitogen-activated protein kinase 4 [Source:HGNC Symbol;Acc:6878]

Sequence

>retro_itri_930
ATGGCAGAGAAATTTGAAAGTCTTATGAACATTCATGGTTTTGATCTGGGCTCTAGGTATATGGACTTAAAACCATTGGG
TTGTGGAGGCAATGGCTTGGTTTTTTCTGCTGTAGACAATGAATGTGACAAAAGAGTAGCCATCAAGAAAATTGTCCTTA
CTGATCCCCAGAGTGTCAAACATGCTCTCCGTGAAATCAAATTATTAGAAGACTTGACCATGATAACATTGTGAAAGTGT
TTAAAATTCTTGGCCCCAGTGGAAGCCAGTTAACAGACGTTGTGGGCTCTCTTACTGAACTGAACAGTGTTTACATTGTT
CAGGAGTACATGGAGACAGACTTGGCTAATGTGCTGGAGCAGGGCCCTTTACTGGAAGAGCATGCCAGGCTTTTCATGTA
TCAGCTGCTACAGGGGCTCAAGTATATTCACTCTGCAAATGTACTGCACAGAGATCTCAAACCAGCTAATCTTTTCATTA
ATACTGAAGACTTGGTGCTGAAGATAGGTGACTTTAGTCTTGCACGGATTATGGATCCTCATTATTCCCATAAGGGTCAG
CTTTCTGAAGGTTTGGTTACTAAATGGTACAGATCTCCACATCTTTTACTTTCTCCTAATAACTATACTAAAGCCATTGA
CATGTGGGCTGCAGGCTGCATCTTTGCTGAAACGCTGACTGGTAAAACCCTCTTTGCAGGTGCACATGAACTTGAACAGA
TGCAACTGATTTTAGAATCTATTCCTGTTGTACATGAGGAAGATCGTTCGGAGCTTCTCAGTGTAATTCCAGTTTACATT
AGAAATGATATGACTGAGCCACACAAACCTTTAACTCAGCTGCTTTCAGGAATTAGTCGAGAAGCACTGGATTTCCTGGA
ACAAATTTTGACATTTAGCCCCATGGATCGATTGACAGCAGAGGAAGCACTCTCTTATCCTTATATGAGTATATATTCTT
TTCCAGTGGATGAGCCAATTTCAAGCCATCCTTTTCACATTGAAGATGAAGTTGATGATATTTTGCTTATGGATGAAACT
CACAGTCACATTTATAACTGGGAAAGGTACCATGATTGTCAGTTTTCAGAGCATGATTGGCCTATACGTAACAACTTCGA
TACTGAT

Alignment

ORF - retro_itri_930 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.58 %
• Parental protein coverage: 62.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAERGDCFASVYGYDLGGRFVDFQPLGFGVNGLVLSATDSHTCRKVAVKKIALSDARSMKHALREIK-II
          MAE.........G.DLG.R..D..PLG.G.NGLV.SA.D......VA.KKI.L.D..S.KHALREIK.II
Retrocopy MAEKFESLMNIHGFDLGSRYMDLKPLGCGGNGLVFSAVDNECDKRVAIKKIVLTDPQSVKHALREIK<II

Parental  RRLDHDNIVKVYEVLGPKG---TDLQGELFKFSVAYIVQEYMETDLARLLEQGTLTEEHAKLFMYQLLRG
          RRLDHDNIVKV...LGP.G...TD..G.L......YIVQEYMETDLA..LEQG.L.EEHA.LFMYQLL.G
Retrocopy RRLDHDNIVKVFKILGPSGSQLTDVVGSLTELNSVYIVQEYMETDLANVLEQGPLLEEHARLFMYQLLQG

Parental  LKYIHSANVLHRDLKPANIFISTEDLVLKIGDFGLARIVDQHYSHKGYLSEGLVTKWYRSPRLLLSPNNY
          LKYIHSANVLHRDLKPAN.FI.TEDLVLKIGDF.LARI.D.HYSHKG.LSEGLVTKWYRSP.LLLSPNNY
Retrocopy LKYIHSANVLHRDLKPANLFINTEDLVLKIGDFSLARIMDPHYSHKGQLSEGLVTKWYRSPHLLLSPNNY

Parental  TKAIDMWAAGCILAEMLTGRMLFAGAHELEQMQLILETIPVIREEDKDELLRVMPAFV-NSTWEVKRPLR
          TKAIDMWAAGCI.AE.LTG..LFAGAHELEQMQLILE.IPV..EED..ELL.V.P....N...E...PL.
Retrocopy TKAIDMWAAGCIFAETLTGKTLFAGAHELEQMQLILESIPVVHEEDRSELLSVIPVYIRNDMTEPHKPLT

Parental  KLLPEVNSEAIDFLEKILTFNPMDRLTAEMGLQHPYMSPYSCPEDEPISQHPFRIEDEIDDIVLMAASQS
          .LL.....EA.DFLE.ILTF.PMDRLTAE..L..PYMS.YS.P.DEPIS.HPF.IEDE.DDI.LM....S
Retrocopy QLLSGISREALDFLEQILTFSPMDRLTAEEALSYPYMSIYSFPVDEPISSHPFHIEDEVDDILLMDETHS

Parental  QLSNWDRYLVC--SSQRYPVSLSSDLE
          ...NW.RY..C..S....P.....D..
Retrocopy HIYNWERYHDCQFSEHDWPIRNNFDTD

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_930 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_930 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000022822	1 retrocopy	retro_itri_930 ,