RetrogeneDB ID: retro_tsyr_1876

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_63455:2208..3224(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000007438
• Aliases: None
• Description: None

Sequence

>retro_tsyr_1876
TCCCAGAAGCAGAGGTCTACGTCCACACCTAATGTCCACATGGTCAGCACCACCCTACTTGTGGACAGCAGGATGATTGA
GGATATAATTCGAAGTCACAGCAAATCAGCCTCATCTTCTGCCCTGTCCAGCAGCCCCAACAATCTGAGCCCACTGGGTT
GGTCACAGTCCAAAACCCCTATGCCAGCACAAAGAGAGCAGGCACCAGGATCCAGGACCCAGGAGAAAAATAAAATTAGG
CCTCGTGGACAAAGAGATTCAAGCTATTACTGGGAAATAGAAGCTAGTGAAGTGATGCTCTCCACTCGGATTGGGTCAGG
CTCCTTTGGGACTGTTTATAAGGGCAAGTGGCATGGAGATGTTGCTGTGACGATCCTAAAGGTTGTCGACCCAACCCCAG
AGCAGTTCCAGGCCTTCAGGAATGAGGTGGCTGTCCTGCGCAAAACACGGCATGTGAACATTCTCCTCTTCATGGGGTAC
ATGACAAAGGACAACCTGGCGATTGTGACCCAGTGGTGCGAGGGCAGCTGCCTCTACAAACACCTGCATGTCCAGGAGAC
CAAGTTTCAGATGTTCCAGTTAATTGACATTGCCCGGCAGATGACTTAGGGGATGGACTATTTGCATGCAAAGAATATCA
TTCACAGAGACATGAAGTCCAACAATATATTTCTCCATGAAGGCCTAACGGTAAAAATTGGAGATTTTGGTTTGGCAACC
GTCAAGTCACGCTAGAGTGACTCTCAGCAGGTTGAACAGCCCACCAGATCCATCTTGTGGATGGCCCCAGAGGTGATCCG
AATGCAGAATAACAACCCGTTCAGGTACAGTACGATGTCTACTATGGCATTGTACTGTACAAGCTGATGACGGGGGAACT
CCCTTACTCCCACATCAATAACTGAGACCAGATCATCTTCATGGTGGGCCGAGGGTATGCCTCCCCAGATCTTAGTAAGC
TATACAAGAACTGCCCCAAAGCAATGAAGAGGCTGGTAGCCGACTGTGTGAAGAAA

Alignment

ORF - retro_tsyr_1876 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.38 %
• Parental protein coverage: 52.47 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SQRQRSTSTPNVHMVSTTLPVDSRMIEDAIRSHSESASPSALSSSPNNLSPTGWSQSKTPVPAQRERAPG
          SQ.QRSTSTPNVHMVSTTL.VDSRMIED.IRSHS.SAS.SALSSSPNNLSP.GWSQSKTP.PAQRE.APG
Retrocopy SQKQRSTSTPNVHMVSTTLLVDSRMIEDIIRSHSKSASSSALSSSPNNLSPLGWSQSKTPMPAQREQAPG

Parental  SGTQEKNKIRPRGQRDSSYYWEIEASEVMLSTRIGSGSFGTVYKGKWHGDVAVKILKVVNPTPEQFQAFR
          S.TQEKNKIRPRGQRDSSYYWEIEASEVMLSTRIGSGSFGTVYKGKWHGDVAV.ILKVV.PTPEQFQAFR
Retrocopy SRTQEKNKIRPRGQRDSSYYWEIEASEVMLSTRIGSGSFGTVYKGKWHGDVAVTILKVVDPTPEQFQAFR

Parental  NEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLIDIARQTAQGMDYLHA
          NEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGS.LYKHLHVQETKFQMFQLIDIARQ...GMDYLHA
Retrocopy NEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSCLYKHLHVQETKFQMFQLIDIARQMT*GMDYLHA

Parental  KNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQVEQPTGSILWMAPEVIRMQDNNPFSF-QSD
          KNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSR.S.SQQVEQPT.SILWMAPEVIRMQ.NNPF...Q.D
Retrocopy KNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSR*SDSQQVEQPTRSILWMAPEVIRMQNNNPFRY<QYD

Parental  VYSYGIVLYELMTGELPYSHINNRDQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADCVKK
          VY.YGIVLY.LMTGELPYSHINN.DQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADCVKK
Retrocopy VY-YGIVLYKLMTGELPYSHINN*DQIIFMVGRGYASPDLSKLYKNCPKAMKRLVADCVKK

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_1876 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
Equus caballus	ENSECAG00000011807	1 retrocopy	retro_ecab_47,
Macaca mulatta	ENSMMUG00000007450	1 retrocopy	retro_mmul_2506,
Tarsius syrichta	ENSTSYG00000007438	1 retrocopy	retro_tsyr_1876 ,