RetrogeneDB ID: retro_itri_755

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393318.1:12594442..12595070(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUP35
• Ensembl ID: ENSSTOG00000000711
• Aliases: None
• Description: nucleoporin 35kDa [Source:HGNC Symbol;Acc:29797]

Sequence

>retro_itri_755
AAGAGTGGAATTCTACTAGTTAGAAGTACGTATGATGACATTTCCTTCCCAGGGCTCATACCAACACCTTGAAATTTAAG
AAGACAGCCAAACATTTCAGTAATGCAGAATAATCTGGTTGGAATTACAAAAACTACTTCTGGAACAGGGAAAAATATAT
TTAATCCATCGAATATTGATCATTCACAAAAGATGACATTAACTCCTGCCAAGTTGGATTCTATTTATACGCCAGAAATT
CCCTGACTTCAGAAGACAACCTGGATGACATTCAGGTGACTGTGTTTTGGTTTCCTCAAGTATCTACTTTCTATATATTA
TTACAATTTGTATAATATGGGACTATCTTAAAACATGTGATGTCTAGAATAGGAAATTGGATGCATATTTGTTACCAATC
TAAACTGCAGGTCCAGAAAGCCTTAGGCAAAGATGGGAGAAACTTTGGAAAATCTGTCATGATTGATGCAAAATGATGAA
TAAATAAAAGTGTTACAGAAAACAGGGATAGATGTGCTTTGTCATCTCCGTCTCTAGCCTTTGTATCACCCATCAAAACC
TTAGGCACACCACTACAACCAGAAGTAGCCCCAGGATTTCTACCATGAAACCTCTTGCTACAGCATTT

Alignment

ORF - retro_itri_755 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.45 %
• Parental protein coverage: 64.22 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KSGAPPVRSIYDDISSPGLGSTPLTSRRQMNISVMQSPLVGVTTTTPGTGQSMFSPANIGQPRKTTLSPA
          KSG...VRS.YDDIS.PGL..TP...RRQ.NISVMQ..LVG.T.TT.GTG...F.P.NI....K.TL.PA
Retrocopy KSGILLVRSTYDDISFPGLIPTP*NLRRQPNISVMQNNLVGITKTTSGTGKNIFNPSNIDHSQKMTLTPA

Parental  QLDPFYTQG-DSLTSEDHLDDTWVTVFGFPQASASYILLQFAQYGNILKHVMSNTGNWMHIRYQSKLQAR
          .LD..YT....SLTSED.LDD..VTVF.FPQ.S..YILLQF..YG.ILKHVMS..GNWMHI.YQSKLQ..
Retrocopy KLDSIYTPE<NSLTSEDNLDDIQVTVFWFPQVSTFYILLQFV*YGTILKHVMSRIGNWMHICYQSKLQVQ

Parental  KALSKDGRIFGESIMIGVKPCIDKSVMENSDRCALSSPSLAFTPPIKTLGTP-TQSGSTPRISTMRPLAT
          KAL.KDGR.FG.S.MI..K..I.KSV.EN.DRCALSSPSLAF..PIKTLGTP.T...S.PRISTM.PLAT
Retrocopy KALGKDGRNFGKSVMIDAK**INKSVTENRDRCALSSPSLAFVSPIKTLGTP<TTTRSSPRISTMKPLAT

Parental  AY
          A.
Retrocopy AF

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_755 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_755 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008469	1 retrocopy	retro_eeur_666,
Homo sapiens	ENSG00000163002	1 retrocopy	retro_hsap_551,
Gorilla gorilla	ENSGGOG00000009919	1 retrocopy	retro_ggor_500,
Macaca mulatta	ENSMMUG00000004140	1 retrocopy	retro_mmul_2387,
Nomascus leucogenys	ENSNLEG00000006423	1 retrocopy	retro_nleu_2019,
Pongo abelii	ENSPPYG00000012998	1 retrocopy	retro_pabe_508,
Pan troglodytes	ENSPTRG00000012711	1 retrocopy	retro_ptro_414,
Ictidomys tridecemlineatus	ENSSTOG00000000711	2 retrocopies	retro_itri_755 , retro_itri_760,