RetrogeneDB ID: retro_itri_818

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393327.1:4383259..4383824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED8
• Ensembl ID: ENSSTOG00000009737
• Aliases: None
• Description: mediator complex subunit 8 [Source:HGNC Symbol;Acc:19971]

Sequence

>retro_itri_818
GAGAAGTAGTTTGGAGTATCATCAGGTGCCCTGTGGAGGCAAGGGGCCGACCTGAGGAGACCACTAGGAAGTTTTCATTT
ACAAGCTGGAGAAAGAGTATGACTGGCTGACCTGGCCCTCTGACCAAGACAGCTTTTCATTGTTCTCTGGAAAGTTAAAC
ACTCTTAACAAAATCCCTAAGCATAAGAAAACACCTGTGTTCCACAACCAGGTCATTTATTCCTCTGGTGTTGTCCCCAG
ACCCAAGATGAAGTTCTCATGTAGCAGATGAAGGAAGGACAAGTACCTGTTTTTAGCCATGAGACAGTCCCTGGCCATCT
GAGAACCAACTTGACCCTAAGGTCGAAGAGCAGGAGAAGCAAGTAGCAGTGGACACTGTCCACATTGGTGTTGATGGAGC
TCAGCAGCAGATTCCAAGCTTGAATAAAATGCACTCAAACCTCTGGAGAAAATCAGCAAGGATGAGTGAGAATCATAAAA
TGAAGGTCTCTGGCCAAACAAGCAGCCCTTTAACCCTGAAGACAGCAATACCTTGGTGGCAGCTGTTGCCTTTGGGAAGG
GGCTA

Alignment

ORF - retro_itri_818 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.88 %
• Parental protein coverage: 69.78 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  EKQLEASLDALLSQVADLKNSLGS-FIYKLENEYDRLTWPSVLDSFALLSGQLNTLNKVLKHEKTPLFRN
          EK....S..AL..Q.ADL...LGS.FIYKLE.EYD.LTWPS..DSF.L.SG.LNTLNK..KH.KTP.F.N
Retrocopy EK*FGVSSGALWRQGADLRRPLGS>FIYKLEKEYDWLTWPSDQDSFSLFSGKLNTLNKIPKHKKTPVFHN

Parental  QVI-IPLVLSPD-RDEDLM-RQTEGRVPVFSHEVVPDHLRT-KPDPEVEEQEKQLTTDAARIGADAAQKQ
          QVI.IPLVLSPD..DE.LM....EG.VPVFSHE.VP.HLRT...DP.VEEQEKQ...D...IG.D.AQ.Q
Retrocopy QVI>IPLVLSPD>QDEVLM*QMKEGQVPVFSHETVPGHLRT<QLDPKVEEQEKQVAVDTVHIGVDGAQQQ

Parental  IQSLNKMCSNL-LEKISKEERESESGGLRPNKQTFNPADTNALVAAVAFGKGL
          I.SLNKM.SNL.LEKISK.E.ES...GL.PNKQ.FNP.D.N.LVAAVAFGKGL
Retrocopy IPSLNKMHSNL<LEKISKDE*ES*NEGLWPNKQPFNPEDSNTLVAAVAFGKGL

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_818 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_818 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005237	1 retrocopy	retro_cfam_458,
Macropus eugenii	ENSMEUG00000013567	1 retrocopy	retro_meug_1813,
Myotis lucifugus	ENSMLUG00000012621	1 retrocopy	retro_mluc_1618,
Monodelphis domestica	ENSMODG00000011310	1 retrocopy	retro_mdom_1131,
Oryctolagus cuniculus	ENSOCUG00000027895	2 retrocopies	retro_ocun_1088, retro_ocun_67,
Otolemur garnettii	ENSOGAG00000001865	1 retrocopy	retro_ogar_2091,
Ictidomys tridecemlineatus	ENSSTOG00000009737	1 retrocopy	retro_itri_818 ,