RetrogeneDB ID: retro_itri_1311

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393436.1:393719..394289(-)
• Located in intron of: ENSSTOG00000011773

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP1A
• Ensembl ID: ENSSTOG00000023813
• Aliases: None
• Description: charged multivesicular body protein 1A [Source:HGNC Symbol;Acc:8740]

Sequence

>retro_itri_1311
CTGTTCAACCTGAAGTTCGCCGCCAAAGAACTGAGCAGGAGTGCCAAGAAGTGCGATAAGGAGGAGAAGGCCGAAAAGGC
CAAGATCAAGAAGGCCATCCAGAAGGGCAACATGGAAGTGGCCCGGATCCACGCCGAGAACGCCATCCGCCAGAAGAACC
AGGCCGTGAACTTCCTGAGGATGAGCGCGCGCGTGGACGCCGTGGCCGCCCGCGTGCAGACGGCCGTGACCATGGGCAAG
GTGACCAAGTCGATGGCCGGCGTGGTCAAGTCCATGGACGCGACGCTGAAGACCATGAACCTGGAGAAGATCTCCGCGCT
GATGGACAAGTTCGAGCACCAGTTCGAGACCCTGGACGTCCAGACGCAGCAGATGGAGGACACGATGAGCAGCACGACGA
CGCTGACCACTCCCCAGAACCAGGTGGACCTGCTGCTCCAGGAGATGGCAGACGAGGCGGGCCTCGACCTCAACATGGAG
CTGCCGCAGGGCCAGACCGGCTCCGTGGGCACCAGCGTGGCCTCGGCCGAGCAGGACGAGCTGTCGCAGAGACTGGCCCG
CCTGCGCGAC

Alignment

ORF - retro_itri_1311 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.25 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALQQKNVECARVYAENAIRKKNEGVNWLRMASRVDAVTS
          LF.LKF.AK.L...AKK..K..KAE.AK.KKA.Q..N.E.AR..AENAIR.KN..VN.LRM..RVDAV..
Retrocopy LFNLKFAAKELSRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARVDAVAA

Parental  KVQMAVTMKGVTKNMAQVTKALDKALSTMDLQKVSAVMDRFEQQVQNLDVHTSVMEDSMSSATTLTTPQE
          .VQ.AVTM..VTK.MA.V.K..D..L.TM.L.K.SA.MD.FE.Q...LDV.T..MED.MSS.TTLTTPQ.
Retrocopy RVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQQMEDTMSSTTTLTTPQN

Parental  QVDSLIVQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
          QVD.L....A.E.GL.....L.Q...G...VG.S......D.LS.RLA.LR.
Retrocopy QVDLLLQEMADEAGLDLNMELPQGQTG--SVGTSVASAEQDELSQRLARLRD

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_1311 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1311 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 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001216	1 retrocopy	retro_amel_1749,
Bos taurus	ENSBTAG00000033331	1 retrocopy	retro_btau_1048,
Canis familiaris	ENSCAFG00000019822	1 retrocopy	retro_cfam_1866,
Callithrix jacchus	ENSCJAG00000010826	1 retrocopy	retro_cjac_1147,
Homo sapiens	ENSG00000131165	2 retrocopies	retro_hsap_359, retro_hsap_75,
Macaca mulatta	ENSMMUG00000014909	3 retrocopies	retro_mmul_1325, retro_mmul_476, retro_mmul_706,
Mustela putorius furo	ENSMPUG00000007281	1 retrocopy	retro_mputfur_383,
Mus musculus	ENSMUSG00000000743	1 retrocopy	retro_mmus_2260,
Oryctolagus cuniculus	ENSOCUG00000023371	1 retrocopy	retro_ocun_1508,
Otolemur garnettii	ENSOGAG00000004883	1 retrocopy	retro_ogar_170,
Pongo abelii	ENSPPYG00000007667	1 retrocopy	retro_pabe_344,
Pan troglodytes	ENSPTRG00000008483	2 retrocopies	retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus	ENSSTOG00000023813	1 retrocopy	retro_itri_1311 ,