RetrogeneDB ID: retro_itri_556

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393301.1:9743150..9743564(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000021288
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBPMS2
• Ensembl ID: ENSSTOG00000010055
• Aliases: None
• Description: RNA binding protein with multiple splicing 2 [Source:HGNC Symbol;Acc:19098]

Sequence

>retro_itri_556
TCGGTCATTGTCAGTGGCCTCCCTGCGGACATTAAACCCAGAGAACTCTACCTGCTCTTCCGGATGTTCAAAGGACATGA
AGGGTCCCTGATCAGGCTCACCTGGAGACAGCCTGTTGGTTTTGTCATCTTTGACAGCCAGGCAGGAGCAGAAGCCTCCA
AGAATGCACTGAAGCCTATTCTCTTTGATCCTGAGAACCCACAAACCCTGAGGCTAGAGTTTGCCAAAGCCAACACCAAG
ATGGCCAAGAGCAAGCTTATTGCAACACCAAATCCCACCAGTGTTCACCCTGCCCTAGGAACACATTTCATCGCCCAGGA
TCCCTATGACCTGATGGGGGCTGCTCTCATCCCTGCATCCCCAGAGGCCTGGGCCCCTTATCCTCTGTACACCACAGAGC
TGACCCCAGCCATC

Alignment

ORF - retro_itri_556 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.41 %
• Parental protein coverage: 76.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLFVSGLPMDIKPRELYLLFRPFKGYEGSLIKLTSRQPVGFVIFDSRAGAEAAKNALNGIRFDPENPQTL
          ...VSGLP.DIKPRELYLLFR.FKG.EGSLI.LT.RQPVGFVIFDS.AGAEA.KNAL..I.FDPENPQTL
Retrocopy SVIVSGLPADIKPRELYLLFRMFKGHEGSLIRLTWRQPVGFVIFDSQAGAEASKNALKPILFDPENPQTL

Parental  RLEFAKANTKMAKSKLMATPNPTSVHPALGAHFIARDPYDLMGAALIPASPEAWAPYPLYTTELTPAI
          RLEFAKANTKMAKSKL.ATPNPTSVHPALG.HFIA.DPYDLMGAALIPASPEAWAPYPLYTTELTPAI
Retrocopy RLEFAKANTKMAKSKLIATPNPTSVHPALGTHFIAQDPYDLMGAALIPASPEAWAPYPLYTTELTPAI

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_556 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_556 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 17 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011037	1 retrocopy	retro_btau_1674,
Callithrix jacchus	ENSCJAG00000005200	2 retrocopies	retro_cjac_1775, retro_cjac_298,
Dipodomys ordii	ENSDORG00000004025	1 retrocopy	retro_dord_438,
Homo sapiens	ENSG00000166831	2 retrocopies	retro_hsap_2513, retro_hsap_3613,
Gorilla gorilla	ENSGGOG00000008984	1 retrocopy	retro_ggor_2438,
Loxodonta africana	ENSLAFG00000018725	6 retrocopies	retro_lafr_344, retro_lafr_393, retro_lafr_445, retro_lafr_481, retro_lafr_550, retro_lafr_859,
Macaca mulatta	ENSMMUG00000013270	1 retrocopy	retro_mmul_1837,
Monodelphis domestica	ENSMODG00000010487	1 retrocopy	retro_mdom_571,
Mus musculus	ENSMUSG00000032387	9 retrocopies	retro_mmus_2671, retro_mmus_3408, retro_mmus_3410, retro_mmus_3429, retro_mmus_3431, retro_mmus_3437, retro_mmus_3562, retro_mmus_3588, retro_mmus_3596,
Nomascus leucogenys	ENSNLEG00000012505	1 retrocopy	retro_nleu_2209,
Otolemur garnettii	ENSOGAG00000026017	1 retrocopy	retro_ogar_3254,
Pongo abelii	ENSPPYG00000006553	1 retrocopy	retro_pabe_2963,
Pan troglodytes	ENSPTRG00000007165	2 retrocopies	retro_ptro_1458, retro_ptro_2441,
Sus scrofa	ENSSSCG00000004549	1 retrocopy	retro_sscr_851,
Ictidomys tridecemlineatus	ENSSTOG00000010055	2 retrocopies	retro_itri_1512, retro_itri_556 ,
Tarsius syrichta	ENSTSYG00000008996	3 retrocopies	retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tursiops truncatus	ENSTTRG00000011840	3 retrocopies	retro_ttru_1046, retro_ttru_1212, retro_ttru_1790,