RetrogeneDB ID: retro_tsyr_1397

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_426018:787..1188(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPMS
• Ensembl ID: ENSTSYG00000013982
• Aliases: None
• Description: RNA binding protein with multiple splicing [Source:HGNC Symbol;Acc:19097]

Sequence

>retro_tsyr_1397
CTGCTCTTCTGGCCTTTCAAGGGGTACGAAGGGTCCCTGATCAAACTCACTGCAAGACAGCCTGTTGGTTTTGTGATCTT
TGACAGCCGGACAGGAGCAGAAGCAGCCAAGAATGCACTGAGCGGTATCCGCTTTGATCCGGAGAACCCGCAGATCCTGA
GGCTAGAGTTTGCCAAAGCCAACACCAAGATGGCCAAGAGCAAGCTAATAGCAACACGGAATCCCAGCAACACGCACCTG
TCCCTCGGAGTACACTTCATTGCATGGTACCCTATGACCTGATGGGGGCAGCTCTGATCCCTGCGTCCCCATAAGCCTGG
GCCCCTTACCCCCTGTACACCACAGAGCTGACCCCAGGCCTCTCCCATGCTGCCTTCACCTCCCCAGCTGCTGCTAACGC
C

Alignment

ORF - retro_tsyr_1397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.44 %
• Parental protein coverage: 71.98 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLFRPF-GYEGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDP--IPTLRLEFAKANTKMAKNKLV
          LLF.PF.GYEGSLIKLT..QPVGFV.FDSR..AEAAKNAL.GIRFDP.....LRLEFAKANTKMAK.KL.
Retrocopy LLFWPFKGYEGSLIKLTARQPVGFVIFDSRTGAEAAKNALSGIRFDPENPQILRLEFAKANTKMAKSKLI

Parental  GTPNPSTPLPNTVPQFIA-REPYELTVPALYPSSPEVWAPYPLYPAELAPALPPPAFTYPASLHA
          .T.NPS.........FIA...PY.L...AL.P.SP..WAPYPLY..EL.P.L...AFT.PA...A
Retrocopy ATRNPSNTHLSLGVHFIA<MVPYDLMGAALIPASP*AWAPYPLYTTELTPGLSHAAFTSPAAANA

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_1397 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001522	1 retrocopy	retro_amel_905,
Bos taurus	ENSBTAG00000033727	1 retrocopy	retro_btau_1555,
Callithrix jacchus	ENSCJAG00000012366	1 retrocopy	retro_cjac_2705,
Tarsius syrichta	ENSTSYG00000008996	3 retrocopies	retro_tsyr_1433, retro_tsyr_171, retro_tsyr_445,
Tarsius syrichta	ENSTSYG00000013982	2 retrocopies	retro_tsyr_1171, retro_tsyr_1397 ,