RetrogeneDB ID: retro_itri_1218

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393404.1:2090948..2091905(-)
• Located in intron of: ENSSTOG00000014530

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE4A
• Ensembl ID: ENSSTOG00000019462
• Aliases: None
• Description: ubiquitination factor E4A [Source:HGNC Symbol;Acc:12499]

Sequence

>retro_itri_1218
CCCATGTATCCCATCCTAAGATACATGTGGGGAACAGATACGTATCGGGAGAGCATTAAGGATTTGGCTGACTATGCCTC
TAAGAATTTAGAAGCTATGAACCCTCCACTTTTCCTCCGCTTTCTTAACCTGCTAATGAATGATGCCATCTTCCTTTTGG
ATGAAGCTATTCAGTATCTGAGCAAGATAAAGATCCAGCAGATTGAGAAGGACCGAGGTGAATGGGATAGTCTGACCCCA
GAAGCTTGCCGAGAGAAAGAGGCTGGCCTGCAGATGTTTGGGCAGTTGGCATGTTTTCATAACATCATGTCCAATGAAAC
AATTGGTACACTTGCCTTCCTAACATCAGAAATCAAATCACTTTTCATGCATCCTTTTCTGGCTGAGCGCATCATCTCTA
TGCTGAACTACTTCCTGCAGCACCTGGTTGGGCCCAAGATGGGTGCCTTAAAAGTCAAGGACTTCAGTGAATTTGACTTC
AAACCCCAGCAGCTTGTATCAGATATCTGCACTATCTACTTAAATCTTGGGGATGAGGAGAATTTCTGTGCCACTGTGCC
CAAGGATGGACGTTCCTATTCCCCAACTCTCTTTGCACAGACAGTTCGAGTCCTGAAGAAAATAAATAAGCCTGGGAATA
TGATTGTGGCTTTTAGTAATCTGGCAGAGAAAATCAAGTCTCTTGCAGACCTCCAACAACAAGAAGAGGAGACCTATGCA
GATGCCTGTGGTGAGTTCCTGGATCCTGTCCTGAGCACACTGATGTCTGACCCTGGGCTGCTGCCGTCCTCCAGAGTCAC
TGTGGATAGATCCACCATTGCCAGACATTCGCTCAGTGACCAAACAGATCCTTTTAACCGCAGTCCCCTCACCATGGACC
AGATCCGGCCAAACCCTGAACTAAAAGAAAAAATCCAACGGTGGCTTGCAGAGAGGAAACAACAGCAAAAGGAGCAA

Alignment

ORF - retro_itri_1218 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.87 %
• Parental protein coverage: 59.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PMYPILRYMWGTDTYRESIKDLADYASKNLEAMNPPLFLRFLNLLMNDAIFLLDEAIQYLSKIKIQQIEK
          PMYPILRYMWGTDTYRESIKDLADYASKNLEAMNPPLFLRFLNLLMNDAIFLLDEAIQYLSKIKIQQIEK
Retrocopy PMYPILRYMWGTDTYRESIKDLADYASKNLEAMNPPLFLRFLNLLMNDAIFLLDEAIQYLSKIKIQQIEK

Parental  DRGEWDSLTPEARREKEAGLQMFGQLARFHNIMSNETIGTLAFLTSEIKSLFVHPFLAERIISMLNYFLQ
          DRGEWDSLTPEA.REKEAGLQMFGQLA.FHNIMSNETIGTLAFLTSEIKSLF.HPFLAERIISMLNYFLQ
Retrocopy DRGEWDSLTPEACREKEAGLQMFGQLACFHNIMSNETIGTLAFLTSEIKSLFMHPFLAERIISMLNYFLQ

Parental  HLVGPKMGALKVKDFSEFDFKPQQLVSDICTIYLNLGDEENFCATVPKDGRSYSPTLFAQTVRVLKKINK
          HLVGPKMGALKVKDFSEFDFKPQQLVSDICTIYLNLGDEENFCATVPKDGRSYSPTLFAQTVRVLKKINK
Retrocopy HLVGPKMGALKVKDFSEFDFKPQQLVSDICTIYLNLGDEENFCATVPKDGRSYSPTLFAQTVRVLKKINK

Parental  PGNMIVAFSNLAEKIKSLADLQQQEEETYADACDEFLDPIMSTLMSDPVVLPSSRVTVDRSTIARHLLSD
          PGNMIVAFSNLAEKIKSLADLQQQEEETYADAC.EFLDP..STLMSDP..LPSSRVTVDRSTIARH.LSD
Retrocopy PGNMIVAFSNLAEKIKSLADLQQQEEETYADACGEFLDPVLSTLMSDPGLLPSSRVTVDRSTIARHSLSD

Parental  QTDPFNRSPLTMDQIRPNTELKEKIQRWLAERKQQQKEQ
          QTDPFNRSPLTMDQIRPN.ELKEKIQRWLAERKQQQKEQ
Retrocopy QTDPFNRSPLTMDQIRPNPELKEKIQRWLAERKQQQKEQ

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_1218 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1218 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	ENSSTOG00000019462	1 retrocopy	retro_itri_1218 ,