RetrogeneDB ID: retro_itri_481

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393294.1:5622374..5623574(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ETFDH
• Ensembl ID: ENSSTOG00000004905
• Aliases: None
• Description: electron-transferring-flavoprotein dehydrogenase [Source:HGNC Symbol;Acc:3483]

Sequence

>retro_itri_481
GATGTGGGAATACAAAAGGATGGCGCACCAAAGACAACATTTGAGCGGGGACTAGAACTACATGCCAAAGTCACAGTTTT
TGCGGAGGGTTGCCTTGGACACCTAGCCAAGCAACTATACAAGAAATTTGATTTGAGGGCCAATTGTGATCCCCAAACAT
ATGGGATTGGACTGAAGGAGTTATGGATTATTGATGAAAAGAAGTGGAAACCTGTGAGAGTGGATCACACAGTTGGATGG
CCCTTGGACAGGCATACTTATGGAGGCCCTTTCCTCTATCATTTAAATGAAGGTGAACCCCTAGTAGCTCTTGGTTTTGT
GGTTGGTCTAGACTATCAAGATCCTTACCCGAATCCATTCAGAGAATTCCAAAGGTGGAAACATCATCCCAGCATTCAGC
CAACATTGGAAGGTGAGAAAAGAATTGCCTATGGAGCCAGAGCTCTCAATGAAGGTGGCTTTCAGTCTATATCAAAACTC
ACCTTTCCTGGTGGTTTACTAATTGGTTGTAGCCCTGGCTTCTTGAATGTTCCCAAGATCAAAGGTATCCATACAGCAAT
GAAAAATAGAAGTTTGGCAGCAGACTCAATTTTTCGTCAACTAACTGGTGAAAATCTCCAATCAAAGACAATAGGACTCC
ATGTAATCAAGTATGAGGACAATTTGAAGAAATCTTGGGTGTGGAAAGAGCTGTATTCTGTTAGAAATATAAGACCTTCC
TGCCATGAAGCATTGGGTTTATATGGAGCGATGATTTACACTGGAATATTTTATTGGATATTGAGAGGAATGGAACCATG
GACCCTAAAACATAAAGGTTCTGACTCTGATCAGCTTAAGCCAGCCAAAGATTGCACAACTACTGAGTATCCAAAACCTG
ATGGACAGATCAGTTTTGACCTCTTGTCATCTGTGGCTTTAAGTGGTACTAATCATGAACATGACCAGCCAGCACATTTA
ACTTTAAAGGATGACAACATACCTATAAACAGAAATCTATCAATATATGATGGGCATGAGCAGTGATTCTGCCCTGCAGG
AGTTTATGAATTTGTACCTTTGGAACAAGGTGATGGATTTCGGTTACAGATAAATGCTCAGAACTATGTGCACTGTAAAA
CATGTGATATTAAAGATCCAAGTCAGAATATTAACTGGATGGTGCCCGAAGTTGGAGGAGGACCAGCTTAAAATGGAATG

Alignment

ORF - retro_itri_481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93. %
• Parental protein coverage: 64.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DVGIQKDGAPKTTFERGLELHAKVTVFAEGCHGHLAKQLYKKFDLRANCDPQTYGIGLKELWIIDEKKWK
          DVGIQKDGAPKTTFERGLELHAKVTVFAEGC.GHLAKQLYKKFDLRANCDPQTYGIGLKELWIIDEKKWK
Retrocopy DVGIQKDGAPKTTFERGLELHAKVTVFAEGCLGHLAKQLYKKFDLRANCDPQTYGIGLKELWIIDEKKWK

Parental  PGRVDHTVGWPLDRHTYGGSFLYHLNEGEPLVALGFVVGLDYQNPYLSPFREFQRWKHHPSIQPTLEGGK
          P.RVDHTVGWPLDRHTYGG.FLYHLNEGEPLVALGFVVGLDYQ.PY..PFREFQRWKHHPSIQPTLEG.K
Retrocopy PVRVDHTVGWPLDRHTYGGPFLYHLNEGEPLVALGFVVGLDYQDPYPNPFREFQRWKHHPSIQPTLEGEK

Parental  RIAYGARALNEGGFQSIPKLTFPGGLLIGCSPGFLNVPKIKGTHTAMKSGSLAAESIFNQLTSENLQSKT
          RIAYGARALNEGGFQSI.KLTFPGGLLIGCSPGFLNVPKIKG.HTAMK..SLAA.SIF.QLT.ENLQSKT
Retrocopy RIAYGARALNEGGFQSISKLTFPGGLLIGCSPGFLNVPKIKGIHTAMKNRSLAADSIFRQLTGENLQSKT

Parental  IGLHVTEYEDNLKKSWVWKELYSVRNIRPSCHGALGLYGGMIYTGIFYWILRGMEPWTLKHKGSDSDQLK
          IGLHV..YEDNLKKSWVWKELYSVRNIRPSCH.ALGLYG.MIYTGIFYWILRGMEPWTLKHKGSDSDQLK
Retrocopy IGLHVIKYEDNLKKSWVWKELYSVRNIRPSCHEALGLYGAMIYTGIFYWILRGMEPWTLKHKGSDSDQLK

Parental  PAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDSIPVNRNLSIYDGPEQRFCPAGVYE
          PAKDCT..EYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDD.IP.NRNLSIYDG.EQ.FCPAGVYE
Retrocopy PAKDCTTTEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDNIPINRNLSIYDGHEQ*FCPAGVYE

Parental  FVPLEQGDGFRLQINAQNCVHCKTCDIKDPSQNINWVVPEGGGGPAYNGM
          FVPLEQGDGFRLQINAQN.VHCKTCDIKDPSQNINW.VPE.GGGPA.NGM
Retrocopy FVPLEQGDGFRLQINAQNYVHCKTCDIKDPSQNINWMVPEVGGGPA*NGM

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_481 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_481 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000004905	1 retrocopy	retro_itri_481 ,
Xenopus tropicalis	ENSXETG00000019489	1 retrocopy	retro_xtro_58,