RetrogeneDB ID: retro_tsyr_1231

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_357899:321..984(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000006215
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSTSYG00000003939
• Aliases: None
• Description: RNA binding motif protein 22 [Source:HGNC Symbol;Acc:25503]

Sequence

>retro_tsyr_1231
ATGGTGGCCTCGCTGGGTTCCAACTCCTACAACAGGCAGAACTGGGAGGATTCGGACTTTCCCACTCTGTGTCAGACGTG
TCTTGGAGAAAACTCTTACACCCGCATGACCAAAGAAAAGTATGGGAAGGAATGAAAATCTGTGCCAGACCATTCACAGT
GTTTCGCTGGTGCCTGGAGACCGCCTGCGTTTCAAGAAGACTGAAGGGTGCCAGACCTGCAGTAAATTGAAGAATGTCTG
TCAGACCTGCCTCTTAGACCTGGAGTATGGCCTGCCCATCCAGGTTTGTGATGCAGGGCTGTCTTTTAAAGATGACATGC
CCAGATCAGATGTCAACAAAGAATACTACACACAGAATATGGAGCGAGAGATTTCTAACTCTGATGGAACACGGCCGGTC
GGCATGCTGGGGAAAGCCACATCCACCAGTGACATGCTGCTCAAGCTGGCCCGGACTACACCCTACTACAAGAGGAATCG
GCCCCACATTTGCTCCTTCTGGGTAAAAGGGTGTGCAAGAGAGGAGAGGAGTGTCCGTACAGACATGAGAAGCCCACAGA
TCCTGATGACACCCTTGCTGATCAGAATATTAAAGACCGATATTATGGAATCAATGACCCTGTGGCTGATAAGCTTCTGA
AGCGGGCCTCAACAATGCCTCGT

Alignment

ORF - retro_tsyr_1231 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.11 %
• Parental protein coverage: 52.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MATSLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKE-CKICARPFTVFRWC-PGVRMRFKKT
          M..SLGSN.YNRQNWED.DFP.LCQTCLGEN.Y.RMTKEKYGKE..KICARPFTVFRWC.PG.R.RFKKT
Retrocopy MVASLGSNSYNRQNWEDSDFPTLCQTCLGENSYTRMTKEKYGKE<MKICARPFTVFRWC<PGDRLRFKKT

Parental  EVCQTCSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQNMEREISNSDGTRPVGMLG
          E.CQTCSKLKNVCQTCLLDLEYGLPIQV.DAGLSFKDDMP.SDVNKEYYTQNMEREISNSDGTRPVGMLG
Retrocopy EGCQTCSKLKNVCQTCLLDLEYGLPIQVCDAGLSFKDDMPRSDVNKEYYTQNMEREISNSDGTRPVGMLG

Parental  KATSTSDMLLKLARTTPYYKRNRPHICSFWVKG-ECKRGEECPYXXXXXXXXXXXXADQNIKDRYYGIND
          KATSTSDMLLKLARTTPYYKRNRPHICSFWVKG..CKRGEECPY............ADQNIKDRYYGIND
Retrocopy KATSTSDMLLKLARTTPYYKRNRPHICSFWVKG<VCKRGEECPYRHEKPTDPDDTLADQNIKDRYYGIND

Parental  PVADKLLKRASTMPR
          PVADKLLKRASTMPR
Retrocopy PVADKLLKRASTMPR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1231 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338, retro_cjac_2471, retro_cjac_3342, retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348, retro_ptro_2898,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231 ,