RetrogeneDB ID: retro_tsyr_2

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_106276:6971..7628(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000003314
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CCDC101
• Ensembl ID: ENSTSYG00000009894
• Aliases: None
• Description: coiled-coil domain containing 101 [Source:HGNC Symbol;Acc:25156]

Sequence

>retro_tsyr_2
ATCCTCCGGAAAGCCCTAGACAAAATCGCTGAAATCAAGTCTCTGTTGGAAGAGAGGCGGATTGCGGCCAAGATTGCAGG
CCTGTACAATGACTCGGAGTCACCTCGGAAGACTCTGCGCAGAGGGGTGTTGATGACCCTACTGCAGCAGTCGGCCATGA
CTCTGCCCCTGTGGATCGGGAAGCCTGGTGACAAGCCTCCACCCCTCTGTGGGGCCATTCCAGCCTCAGGTGACTATGTG
GCCAAACCTGGATACAAGGTGGCTGCCCGGGTAAAGGCTGTGGATGGGGATGAGCAGTGGATCCTGACTGAGGTGGTCAG
TTACAGCCACGCCACCAACAAGTATGAAGTAGATGACATTGATGAAGAAGGCAAAGAGAGACATACCCTGAGCCGGCCGC
GGATCATCCCTCTGCCCCAGTGGAAGGCCAACCCTGAGACGGACCCCGAGGCCTTATTCCAGAAGGAGCAGCTCGTGCTG
GCCCTGTATCCCCAGACCACTTGCTTCTACCGGGCCCTGATCCATGCACCCCCACAACGGCCTCAGGATGACTACTCGGT
CCTATTTGAGGACACCTCCTACGCAGATGGTTATTCCCCTCCCCTCAATGTGGCCCAGAGGTATGTGGTGGCTTGTAAAG
AGCCCAAGAAAAAGTGA

Alignment

ORF - retro_tsyr_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.82 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTHREVLLTLPL-IRKPGEKPP--LETIPASGDYLVKLGDKVVALVVKAMDGDEQCILAEVVHYSHATPM
          T.......TLPL.I.KPG.KPP.....IPASGDY..K.G.KV.A.V.KA.DGDEQ.IL.EVV.YSHAT..
Retrocopy TLLQQSAMTLPLWIGKPGDKPPPLCGAIPASGDYVAKPGYKVAARV-KAVDGDEQWILTEVVSYSHATNK

Parental  YEVDDMDEEGEERRNLSWRKINPSPQWKAN--TNPEALFQKRKLIVALYPQTTC--HALIHAPPQRPQVD
          YEVDD.DEEG.ER..LS...I.P.PQWKAN..T.PEALFQK..L..ALYPQTTC...ALIHAPPQRPQ.D
Retrocopy YEVDDIDEEGKERHTLSRPRIIPLPQWKANPETDPEALFQKEQLVLALYPQTTCFYRALIHAPPQRPQDD

Parental  YSVLC-DTSYTDGSSCVLNVAQRYMVSCKEPKKK
          YSVL..DTSY.DG.S..LNVAQRY.V.CKEPKKK
Retrocopy YSVLFEDTSYADGYSPPLNVAQRYVVACKEPKKK

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_2 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000015642	1 retrocopy	retro_mdom_939,
Sarcophilus harrisii	ENSSHAG00000011279	1 retrocopy	retro_shar_681,
Tarsius syrichta	ENSTSYG00000009894	1 retrocopy	retro_tsyr_2 ,