RetrogeneDB ID: retro_itri_163

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393531.1:1397508..1398825(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000023186
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: USP22
• Ensembl ID: ENSSTOG00000023814
• Aliases: None
• Description: ubiquitin specific peptidase 22 [Source:HGNC Symbol;Acc:12621]

Sequence

>retro_itri_163
ATGTGTAAGGACTATGTGTATGACAAAGACATTGAGCAAATTGCCAAAGAAGAGCAAGGAGAAGCCTTGAAATTACAAGC
CTCCACCTCAACAGAGGTTTCTCACCAGCAGTGTTCAGTCCCAGGTCTTGGTGAGAAATATCCAACCTGGGAAACAACCA
AACCGGAGTTAGAACTGCTGGGGCACAACCCGCGGCGGAGAAGAATCACGTCCAGCTTCACCATCGGCTTAAGAGGACTA
ATCAATCTCGGCAACACGTGCTTTATGAACTGCATCGTCCAGGCCCTGACCCACACTCCCATCCTGAGAGATTTCTTCCT
CTCCGACAGGCACCGATGTGAAATGCCAAGTCCTGAGTTGTGTCTGGTCTGTGAGATGTCTTCGCTGTTTCGGGAGTTGT
ATTCTGGAAACCCGTCTCCTCACGTTCCCTATAAGTTACTGCACCTGGTGTGGATACATGCTCGCCACTTAGCAGGGTAC
AGGCAACAGGATGCCCACGAGTTCCTCATTGCGGCATTAGATGTCCTGCACAGGCACTGCAAAGGTGATGATGTAGGGAA
GGCAGCCAATAATCCCAACCACTGTAACTGCATCATAGACCAAATCTTCACAGGTGGCCTGCAGTCTGATGTCACCTGTC
AAGCCTGCCATGGGGTCTCCACCACCATAGACCCATGCTGGGACATCAGTTTGGACTTACCTGGCTCTTGCACCTCCTTC
TGGCCTATGAGTCCAGGGAGGGACAGCAGTGTGAATGGGGAAAGCCACATACCAGGCATCACCACCCTCACAGACTGCTT
GAGAAGGTTTACGAGGCCAGAGCACTTAGGAAGCAGTGCCAAAATCAAATGTGGCAGTTGCCAAAGCTACCAGGAATCAA
CCAAACAGCTCACGATGAATAAATTACCAGTTGTTGCCTGTTTTCATTTCAAACGGTTTGAACACTCAGCCAAACAGAGG
CGCAAGATCACTACATACATTTCCTTTCCTCTGGAGCTGGATATGACACCGTTTATGGCCTCAAGTAAAGAGAGCAGAAT
GAATGGACAGTTGCAGCTGCCAACTAATAGTGGAAACAACGAGAATAAGTATTCCTTGTTTGCTGTGGTTAATCACCAAG
GAACCTTGGAGAGTGGCCACTACACCAGCTTCATCCGGCACCACAAGGACCAGTGGTTCAAATGTGATGATGCTGTCATC
ACCAAGGCCAGTATTAAGGATGTGCTGGACAGTGAAGGGTATTTACTGTTCTATCACAAACAGGTCCTGGAACATGAGTC
AGAAAAAGTGAAAGAAATGAATACACAAGCCTACTGA

Alignment

ORF - retro_itri_163 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.34 %
• Parental protein coverage: 77.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEQRKAWKMQGAGEKFSTWEPTKRELELLKHNPKRRKITSNCTIGLRGLINLGNTCFMNCIVQALTHTPL
          E.........G.GEK..TWE.TK.ELELL.HNP.RR.ITS..TIGLRGLINLGNTCFMNCIVQALTHTP.
Retrocopy EVSHQQCSVPGLGEKYPTWETTKPELELLGHNPRRRRITSSFTIGLRGLINLGNTCFMNCIVQALTHTPI

Parental  LRDFFLSDRHRCEMQSPSSCLVCEMSSLFQEFYSGHRSPHIPYKLLHLVWTHARHLAGYEQQDAHEFLIA
          LRDFFLSDRHRCEM.SP..CLVCEMSSLF.E.YSG..SPH.PYKLLHLVW.HARHLAGY.QQDAHEFLIA
Retrocopy LRDFFLSDRHRCEMPSPELCLVCEMSSLFRELYSGNPSPHVPYKLLHLVWIHARHLAGYRQQDAHEFLIA

Parental  ALDVLHRHCKGDDNGKKANNPNHCNCIIDQIFTGGLQSDVTCQVCHGVSTTIDPFWDISLDLPGSSTPFW
          ALDVLHRHCKGDD.GK.ANNPNHCNCIIDQIFTGGLQSDVTCQ.CHGVSTTIDP.WDISLDLPGS.T.FW
Retrocopy ALDVLHRHCKGDDVGKAANNPNHCNCIIDQIFTGGLQSDVTCQACHGVSTTIDPCWDISLDLPGSCTSFW

Parental  PLSPGSEGSVVNGESHTSGTTTLTDCLRRFTRPEHLGSSAKIKCSGCHSYQESTKQLTMKKLPIVACFHL
          P.SPG...S.VNGESH..G.TTLTDCLRRFTRPEHLGSSAKIKC..C.SYQESTKQLTM.KLP.VACFH.
Retrocopy PMSPGRDSS-VNGESHIPGITTLTDCLRRFTRPEHLGSSAKIKCGSCQSYQESTKQLTMNKLPVVACFHF

Parental  KRFEHSAKLRRKITTYVSFPLELDMTPFMASSKESRMNGQYQQPTDSLSNDNKYSLFAVVNHQGTLESGH
          KRFEHSAK.RRKITTY.SFPLELDMTPFMASSKESRMNGQ.Q.PT.S..N.NKYSLFAVVNHQGTLESGH
Retrocopy KRFEHSAKQRRKITTYISFPLELDMTPFMASSKESRMNGQLQLPTNSGNNENKYSLFAVVNHQGTLESGH

Parental  YTSFIRQHKDQWFKCDDAIITKASIKDVLDSEGYLLFYHKQFLEYE
          YTSFIR.HKDQWFKCDDA.ITKASIKDVLDSEGYLLFYHKQ.LE.E
Retrocopy YTSFIRHHKDQWFKCDDAVITKASIKDVLDSEGYLLFYHKQVLEHE

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_163 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_163 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008978	1 retrocopy	retro_btau_82,
Canis familiaris	ENSCAFG00000018523	1 retrocopy	retro_cfam_125,
Homo sapiens	ENSG00000124422	1 retrocopy	retro_hsap_26,
Microcebus murinus	ENSMICG00000009998	1 retrocopy	retro_mmur_1,
Mus musculus	ENSMUSG00000042506	1 retrocopy	retro_mmus_239,
Otolemur garnettii	ENSOGAG00000015801	1 retrocopy	retro_ogar_274,
Pan troglodytes	ENSPTRG00000008891	1 retrocopy	retro_ptro_44,
Pteropus vampyrus	ENSPVAG00000001934	1 retrocopy	retro_pvam_905,
Ictidomys tridecemlineatus	ENSSTOG00000023814	1 retrocopy	retro_itri_163 ,