RetrogeneDB ID: retro_tsyr_1554

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_48788:9597..10443(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC85C
• Ensembl ID: ENSTSYG00000008914
• Aliases: None
• Description: coiled-coil domain containing 85C [Source:HGNC Symbol;Acc:35459]

Sequence

>retro_tsyr_1554
AAGCTTGTTGTTGCGGCAGCAGCAGCGGCACGGAGGCTCGTGCCGGATCAGAAGCTGCTCCGCTGGGGCAAGGAGGAGCT
GGCGTGGCGCCTGTGACCCGCAGAGGGTGATAAGGAGGGCCTCATGCTGGAGCACTGCGGCCTGATGTGCGACGTGAACC
AGAGGCTGCAGCAGCACCTGCTGGAGATCCGCGGGCTCCAGAACGTGAACCAGCAGCTGCACCGCGACAATCAGGAGCTG
CGTGATCTCTGCTTCTTCCTGGACGATGACCCGCAGAAGGGGCGCAAGCTGGCGCACCAGTGGAGGTTTCTGGGCCAAGC
GACCGGCGCCTTGTGGCACTAAGCCGTCCCCTGGCAGCAGAAGCTGCACGAGCTGGAGGTGCGCCAGGAGGCCCTGCTGC
GCGAGAACTTGGAATTCAAGGAACTGGTGCTGCTGCTGAAGGAGGAGAGCGCAGTGTTGGCGGCGGCGGCGGTTCAGGCA
GCTGCATCCACAGCCAGGGCAGTCTGAGTGGGCCGCTGGTAGGCGGCGCGGCTGGTGCTGGGGCCTACGACGTGGACAAC
GGCAGCAGCACGTTGTGAACGGGCAGTGGCGGCAGCCCAGACTAATATCACCACGTCAAGACCTCGCTTCTGCCCTGGGC
CACACAAGGTCCCCAAAGGCAAGGCAGGCGCCACACGGCTATCCCTGGACAACCTGTAGGCGCCACCCTACCAACCCAGC
ATCCCTGACGGCCTGCAAGATCCCTCGTCCACCTACCTCAAAAGGCTGGAGATCAAAGTGAGGATCCTGGAGGGTAACAA
GTTCCTGGCACAGGTAGGGGGTGGCTGGCAGCGGCTGGACCTAAGG

Alignment

ORF - retro_tsyr_1554 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.86 %
• Parental protein coverage: 69.8 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KFVVAAAAAAQSLVPDQKLLCWGKEELAWRL-PAEGDKEGLMLEHCGLMCDVKQRLQQHLLEIRGLQNVN
          K.VVAAAAAA..LVPDQKLL.WGKEELAWRL.PAEGDKEGLMLEHCGLMCDV.QRLQQHLLEIRGLQNVN
Retrocopy KLVVAAAAAARRLVPDQKLLRWGKEELAWRL*PAEGDKEGLMLEHCGLMCDVNQRLQQHLLEIRGLQNVN

Parental  QQLHRDNQELRDLCFFLDDDPQKGRKLAHQW--FWQATGALWH-AVPWQQKLHELEVRQEALLRENLEFK
          QQLHRDNQELRDLCFFLDDDPQKGRKLAHQW....QATGALWH.AVPWQQKLHELEVRQEALLRENLEFK
Retrocopy QQLHRDNQELRDLCFFLDDDPQKGRKLAHQWRFLGQATGALWH*AVPWQQKLHELEVRQEALLRENLEFK

Parental  ELVLLLKEERSV-GGG-GGSGSCIHSQGSLSGPLVGDAAGAGAYYVDDGSSTL-TDSGGSPD-HHHVKTS
          ELVLLLKEE..V..GG.GGSGSCIHSQGSLSGPLVG.AAGAGAY.VD.GSSTL.T.SGGSPD..HHVKTS
Retrocopy ELVLLLKEESAV<VGGGGGSGSCIHSQGSLSGPLVGGAAGAGAYDVDNGSSTL*TGSGGSPD*YHHVKTS

Parental  LLPL-PHKVPKGKAGATRLSLDYLPAPPHHRSIPKGLQDPSSTYLKRLQTQVRVLEGNKFLAQQAGPGEY
          LLP..PHKVPKGKAGATRLSLD.L.APP...SIP.GLQDPSSTYLKRL...VR.LEGNKFLAQ..G....
Retrocopy LLPW>PHKVPKGKAGATRLSLDNL*APPYQPSIPDGLQDPSSTYLKRLEIKVRILEGNKFLAQVGGGWQR

Parental  RTLR
          ..LR
Retrocopy LDLR

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_1554 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Tarsius syrichta	ENSTSYG00000008914	1 retrocopy	retro_tsyr_1554 ,