RetrogeneDB ID: retro_itri_1276

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393423.1:1675862..1677115(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000015494
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AP3M1
• Ensembl ID: ENSSTOG00000012881
• Aliases: None
• Description: adaptor-related protein complex 3, mu 1 subunit [Source:HGNC Symbol;Acc:569]

Sequence

>retro_itri_1276
ATGATCCAGAGTCTGTTTCTCATAAACTGTTCCGGTGACATATTTCTAGAGAAGCACTGGAAGAGTGTTGTGAGCCAATC
TGTCTGTGATTATTTCTTTGAAGCTCAGGAGAAAGCTGCTGATGTTGAAAATGTACCACCTGTCATTTCAACACCTCACC
ACTACCTCATCAGTATCTACCAAGATAAGCTCTTCTTTGTGTCTGTCATACAGACTGAAGTGCCACCTCTCTTTGTTATT
GAGTTCCTACATCGAGTTGCTGACACTTTTCAGGACTACTTTGGTGAGTGTTCGGAGGCTGCAATTAAGGATAATGTGGT
CATAGTATATGAGCTCTTGGAAGAAATGTTAGACAACGGATTTCCACTGGCAACAGAGTCTAACATTTTGAAAGAACTGA
TTAAACCACCAACAATTCTTCGTTCTGTTGTCAGCTCTATTACAGGCAGTAGTAATGTTGGGGACACACTCCCCACTGGG
CAGCTGTCCAACATTCCAGGGCACCAGGTAGGAATAGAATACACAAACAATGAAGCCTATTTTGATGTTGTTGAAGAAAT
AGATGCAATTTTAGGTAAATCAGGATCTACAGTCTTTGCAGAAATTCAAGGAGTCATTGATGCTTGCATTAAGCTATCTG
GAATGCCCAATCTCTCTCTCTCTTTCATGAACCCAAGGCTTCTAGATGATGTCAGTTTCCACCCCTGCATCCGATTCAAG
TGTTGGGAATCTGAACGAGTTTTGTCATTTATCCCTCCAGATGGAAATTTCCGACTCATATCATATCGTGTCAGCTCACA
AAATCTAGTGGCAATACCAGCGTATGTGAAACACAGTATTAGCTTTAAAGAGAACAGTTCTTGTGGCAGATTTGATATAA
CAATTGGACCAAAGCAAAATATGGGAAAACTATTGAAGGAATTACAGTGACAGTTCACATGCCAAAAGTTGTGCCGAATA
TGAACCTGACACCAACACAAGGCAGCTATACATTTGATCCAGTCACTAAGGTATTAACATGGGATGTGGGGAAAATCACT
CCACAAAAGCTTCCAAGTCTTAAAGGACTGGTAAATTTACAGTCTGGAGCACCCAAGCCAGAAGAGAATCCTAGCCTCAA
CATACAGTTCAAGATCCAGCAGCTTGCTATTTCAGGCTTAAAAGTAAACCGCTTGGACATGTATGGGGAGAAGTATAAGC
CATTTAAAGGAGTCAAGTATGTCACGAAAGCTGGAAAGTTTCAAGTGAGGACA

Alignment

ORF - retro_itri_1276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIHSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYQDKLFFVSVI
          MI.SLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYQDKLFFVSVI
Retrocopy MIQSLFLINCSGDIFLEKHWKSVVSQSVCDYFFEAQEKAADVENVPPVISTPHHYLISIYQDKLFFVSVI

Parental  QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTIL
          QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTIL
Retrocopy QTEVPPLFVIEFLHRVADTFQDYFGECSEAAIKDNVVIVYELLEEMLDNGFPLATESNILKELIKPPTIL

Parental  RSVVNSITGSSNVGDTLPTGQLSNIPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACI
          RSVV.SITGSSNVGDTLPTGQLSNIP....G..YTNNEAYFDVVEEIDAI..KSGSTVFAEIQGVIDACI
Retrocopy RSVVSSITGSSNVGDTLPTGQLSNIPGHQVGIEYTNNEAYFDVVEEIDAILGKSGSTVFAEIQGVIDACI

Parental  KLSGMPDLSLSFMNPRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVAIPVYVKHSI
          KLSGMP.LSLSFMNPRLLDDVSFHPCIRFK.WESERVLSFIPPDGNFRLISYRVSSQNLVAIP.YVKHSI
Retrocopy KLSGMPNLSLSFMNPRLLDDVSFHPCIRFKCWESERVLSFIPPDGNFRLISYRVSSQNLVAIPAYVKHSI

Parental  SFKENSSCGRFDITIGPKQNM-GKTIEGITVTVHMPKVVLNMNLTPTQGSYTFDPVTKVLTWDVGKITPQ
          SFKENSSCGRFDITIGPKQNM.GKTIEGITVTVHMPKVV.NMNLTPTQGSYTFDPVTKVLTWDVGKITPQ
Retrocopy SFKENSSCGRFDITIGPKQNM<GKTIEGITVTVHMPKVVPNMNLTPTQGSYTFDPVTKVLTWDVGKITPQ

Parental  KLPSLKGLVNLQSGAPKPEENPSLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYVTKAGKFQVRT
          KLPSLKGLVNLQSGAPKPEENPSLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYVTKAGKFQVRT
Retrocopy KLPSLKGLVNLQSGAPKPEENPSLNIQFKIQQLAISGLKVNRLDMYGEKYKPFKGVKYVTKAGKFQVRT

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_1276 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1276 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004510	1 retrocopy	retro_chof_2586,
Monodelphis domestica	ENSMODG00000000660	1 retrocopy	retro_mdom_1564,
Mus musculus	ENSMUSG00000021824	1 retrocopy	retro_mmus_580,
Ictidomys tridecemlineatus	ENSSTOG00000012881	1 retrocopy	retro_itri_1276 ,