RetrogeneDB ID: retro_itri_1902

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH398260.1:524..1209(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM23
• Ensembl ID: ENSSTOG00000010354
• Aliases: None
• Description: RNA binding motif protein 23 [Source:HGNC Symbol;Acc:20155]

Sequence

>retro_itri_1902
AACACCAGCTTTTGCTTGGCTTTGGGGGGAAATTGGCCACTTCAGATGACTGACAGCATTCAGGGCTCTGTGAAGAAGAG
GAGTCGGAGTCATAGTAGAAGCAGGGATAGAAAGCACAGTCGCAGCCGAGAACGGGATCTGGCATAGATGGAGAAACAGT
CGCAGCCGAAGTCGAGATCCGCAGCGTCATCACCACAGCCGCAGCCATAGCTGGGATCGGCGACATAATAGTGAGTCACG
AAGCCGAGACCGGCGACCTGAAGATCGTGTGCGCTATAGGAGTCCTCCACTTCCCACTGGACGTAGGTATGGACACAGTA
AGAGCCCTCGTTTCAAAGAGAAGAGCCCGGTCAGGTAGCCAATTGATAATCTGAGCCCTGAGGAGCGTGATGCCCGCACA
GTTTTCTGTATGCAATTAGCTGCCCGTATCTGGCCTCGAGACCTGGAGGACTTTTTTTCTGCTGTTGGCAAGGTTGATTA
TGTGTGTATCATCTCAGATCGGAACTCACGTCGTTCTAAAGGCATTCCGTATGTAGAATTCTGTGAAATGCAGTCTGTGC
CACTGGCCATTGGGCTGACTGGGCAACGACTTCTGGGAGTACCTATCATTGTACAGGCCTCACAGGCTGAGAAAAACCGA
CTGGCAGCCATGGCCAACAATCTGCAGAAGGGTACTGGTGGACCA

Alignment

ORF - retro_itri_1902 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.84 %
• Parental protein coverage: 51.02 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NTTSNTGNSGSGTSVSTTTGETSKKKRSRSHSRSRDRKCS--RSRDR-HRRRNSRSRSRDRQRHHRSRSR
          NT.......G......T.....S.KKRSRSHSRSRDRK.S..R.RD..HR.RNSRSRSRD.QRHH.SRS.
Retrocopy NTSFCLALGGNWPLQMTDSIQGSVKKRSRSHSRSRDRKHSRSRERDL>HRWRNSRSRSRDPQRHHHSRSH

Parental  SWDRRHNSESRSRDRRREDRVRYRSPPLPTGRRYGHSKSPHFKEKSPVRQPIDNLSPEERDARTVFCMQL
          SWDRRHNSESRSRDRR.EDRVRYRSPPLPTGRRYGHSKSP.FKEKSPVR.PIDNLSPEERDARTVFCMQL
Retrocopy SWDRRHNSESRSRDRRPEDRVRYRSPPLPTGRRYGHSKSPRFKEKSPVR*PIDNLSPEERDARTVFCMQL

Parental  AARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEMQSVPLAIGLTGQRLLGVPIIVQASQA
          AARI.PRDLEDFFSAVGKV..V.IISDRNSRRSKGI.YVEFCEMQSVPLAIGLTGQRLLGVPIIVQASQA
Retrocopy AARIWPRDLEDFFSAVGKVDYVCIISDRNSRRSKGIPYVEFCEMQSVPLAIGLTGQRLLGVPIIVQASQA

Parental  EKNRLAAMANNLQKGTGGP
          EKNRLAAMANNLQKGTGGP
Retrocopy EKNRLAAMANNLQKGTGGP

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_1902 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1902 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008482	1 retrocopy	retro_cjac_1069,
Myotis lucifugus	ENSMLUG00000012923	1 retrocopy	retro_mluc_2430,
Ochotona princeps	ENSOPRG00000001092	2 retrocopies	retro_opri_126, retro_opri_412,
Pan troglodytes	ENSPTRG00000006151	1 retrocopy	retro_ptro_3108,
Ictidomys tridecemlineatus	ENSSTOG00000010354	1 retrocopy	retro_itri_1902 ,