RetrogeneDB ID: retro_tsyr_741

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_186564:3941..4520(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNJ
• Ensembl ID: ENSTSYG00000009466
• Aliases: None
• Description: cyclin J [Source:HGNC Symbol;Acc:23434]

Sequence

>retro_tsyr_741
ATGGAGCTGGAGGGGCAGTGGTGGCGAGGACAGCTGGCCGCCAACATGCACCAGGCGCTTCAGTACAAGGAGCTGAAGTT
GCCCTCCTACAAAGGCCAGTCCCCTCAACTAAGTCTCAGGCGGTATTTTGCTGACTTGATTGCCATTGTGAGCAATCGCT
TTACACTCTGCCCATCTGCCCAACATCTTGCTGTCTATTTGCTGGACTTGTTTATGGATCGCTATGACATCTCTATCCAA
CAGCTCTATCTAGTTGCGCTTTCCTGTCTGCTTCTAGCAAGTAAGTTTGAAGAGAAGGAAGACAGCGTGCCTAAGCTGGA
GCAGCTCAACAGCCTGGGCTGCATGACCAACATGAATCTCGTATTAACAAAACAAAACTTGCTACACATGGAACTCTTAC
TATTAGAAACCTTCCAGTGGAACCTCTGCCTGCCGACAGCTGCCCATTTCATCAAGTATTATCTCTCTGAAGCTGTACAT
GAAATGGATCTTCATGATGGCTGGCCCATGATTTGCTTGGAAAAAACTAAACTCTACATGGCCAAGTATGCAGATTATTT
CCTGGAAGTGTCTTTGCAA

Alignment

ORF - retro_tsyr_741 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.85 %
• Parental protein coverage: 51.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MELEGQWWRGQLAADIHQALRYKELKLPSYKGQSPQLSLRRYFADLIAIVSNRFTLCPSARHLAVYLLDL
          MELEGQWWRGQLAA..HQAL.YKELKLPSYKGQSPQLSLRRYFADLIAIVSNRFTLCPSA.HLAVYLLDL
Retrocopy MELEGQWWRGQLAANMHQALQYKELKLPSYKGQSPQLSLRRYFADLIAIVSNRFTLCPSAQHLAVYLLDL

Parental  FMDRYDISIQQLHLVALSCLLLASKFEEKEDSVPKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETFQW
          FMDRYDISIQQL.LVALSCLLLASKFEEKEDSVPKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETFQW
Retrocopy FMDRYDISIQQLYLVALSCLLLASKFEEKEDSVPKLEQLNSLGCMTNMNLVLTKQNLLHMELLLLETFQW

Parental  NLCLPTAAHFIEYYLSEAVHETDLHDGWPMICLEKTKLYMAKYANYFLEVSLQ
          NLCLPTAAHFI.YYLSEAVHE.DLHDGWPMICLEKTKLYMAKYA.YFLEVSLQ
Retrocopy NLCLPTAAHFIKYYLSEAVHEMDLHDGWPMICLEKTKLYMAKYADYFLEVSLQ

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_741 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016259	1 retrocopy	retro_cjac_3274,
Erinaceus europaeus	ENSEEUG00000002270	2 retrocopies	retro_eeur_535, retro_eeur_577,
Homo sapiens	ENSG00000107443	1 retrocopy	retro_hsap_3850,
Gorilla gorilla	ENSGGOG00000006034	1 retrocopy	retro_ggor_2595,
Oryctolagus cuniculus	ENSOCUG00000011114	1 retrocopy	retro_ocun_425,
Tarsius syrichta	ENSTSYG00000009466	1 retrocopy	retro_tsyr_741 ,