RetrogeneDB ID: retro_itri_1029

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393360.1:720106..720549(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APIP
• Ensembl ID: ENSSTOG00000004390
• Aliases: None
• Description: APAF1 interacting protein [Source:HGNC Symbol;Acc:17581]

Sequence

>retro_itri_1029
AGCCAGTGCAATCCTCTTTTCATAAATTCTTACACAATGAGAGGAGCAGGTGCAGTGATTCAAATCCACTCTAAAGCTGC
TGTGATGGCCACCCTCCTCTTTCCAGGATGAGAGTTTAAAATTACACATCCAGAGGTGATCAAAGGAATAAGGCAATGTA
TCTCAGGAGGGTATTTTAGATATGATGATATGTTAGTGGCACCTATTATTGAGAGCACAACTGAAGAACAAGACCCCAAA
GAACTAAAGGCCCGTCAATGAATGAATATCCCGACTCCTGTGCAGTACTGGTCAGGTGTCATGGAGTGTATGTCGGGAGA
GATACTAGGAGAAAGCTAAAAATCACACGTGAATGTTATGACTATTTTATTGACATTGCTGTAATAATGATGAAGGTAGG
ACTTGATCCTATGCAGCTCCCAGTTGGAGAAAATAGAATTGTA

Alignment

ORF - retro_itri_1029 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.39 %
• Parental protein coverage: 61.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQCTPLFMNAYTMRAPTYLIYTHPKAVISGTTLEFGVVFQIKREYLTGNLKKNGSFCLHRYDDMLVVPII
          SQC.PLF.N.YTMR.....I..H.KA....T.L..G..F.I.............S....RYDDMLV.PII
Retrocopy SQCNPLFINSYTMRGAGAVIQIHSKAAVMATLLFPG*EFKITHPEVIKGIRQCISGGYFRYDDMLVAPII

Parental  ENTPEEKDLKERMAR-AMNEYPDSCAVLVRRHGVYVWGDTWEKAKTMCECYDYLFDIAVSMKKVGLDPTQ
          E.T.EE.D.KE..AR..MNEYPDSCAVLVR.HGVYV..DT..K.K...ECYDY..DIAV.M.KVGLDP.Q
Retrocopy ESTTEEQDPKELKAR<SMNEYPDSCAVLVRCHGVYVGRDTRRKLKITRECYDYFIDIAVIMMKVGLDPMQ

Parental  LPVGENGIV
          LPVGEN.IV
Retrocopy LPVGENRIV

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_1029 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1029 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000016758	1 retrocopy	retro_etel_220,
Homo sapiens	ENSG00000149089	1 retrocopy	retro_hsap_4208,
Gorilla gorilla	ENSGGOG00000022940	2 retrocopies	retro_ggor_2818, retro_ggor_2873,
Ornithorhynchus anatinus	ENSOANG00000007394	6 retrocopies	retro_oana_108, retro_oana_109, retro_oana_121, retro_oana_63, retro_oana_85, retro_oana_96,
Pongo abelii	ENSPPYG00000003361	1 retrocopy	retro_pabe_3442,
Pan troglodytes	ENSPTRG00000003499	1 retrocopy	retro_ptro_2856,
Sarcophilus harrisii	ENSSHAG00000011523	1 retrocopy	retro_shar_574,
Ictidomys tridecemlineatus	ENSSTOG00000004390	1 retrocopy	retro_itri_1029 ,