RetrogeneDB ID: retro_tsyr_1134

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_31771:6796..7608(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1C1
• Ensembl ID: ENSTSYG00000006233
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 [Source:HGNC Symbol;Acc:856]

Sequence

>retro_tsyr_1134
ATGACTGAATTCTTGCTTATATTTGCTCCTGGAGAGAAAAATCTGTCAGCAAACATGGGAGAAACTACATGTGGCAACTA
CGAAGAACAATAATCTTGCTGTCACCTCCAAGTTCAACATTCCTGACTTAAGAGTTGGCACACTGAACATCTTGGTTGGC
CTGTCAGATGAACTGGCTAAAGTGGATGCATTTGTAGAAGGAGTGATTAAGAAAGTGGCTCAATACATGGCTGATGTATT
GGAGGATAATAAAGATAAATTTCAGGAGTATCTGCTGGCCAATGGAGTTGACTTGCTTGCTTATATAGCAAGATTCCAAT
GGGATATGGCCAAGTATCCAATCATGCAAGTCCTGAAAAATATTTCTGAAATAATTGCTAAGAGAATAACTCAGATTGAT
AATGTCCTGAAATCTCAAGCATCTACATTCAATAACCTGAAAAGGAACCTTCAGAACTTGGAGTGAAAGAATGCAGGGTT
TGCTAACTAGAAGTCTGGCAGGAATTGTGAAGAAGGATGACTTTGTTCTTGATTCAGAGTATCTTGTCACATTACTGGTG
GCAGTTCCCAAGTTAAAACACAATGCCTGGATTAAGCAGTATGAAACACTAGCTGAAATAGTTGTTCCAAGGTCTAGCCA
TGTGCTTTCAGAGGACCAAGGCAGTTACCTTTGTAATGTCACCTTGTTCAGCAAGGCAGTTGATGACTTCAGACATAAAG
CAAGGGAAAACAAATTCCTTGTTCATGGCTTTCAGTATAATGAAGAGGAGATGAAAGCAGATAAAGAAGAAATGAGCAGG
TTTTCCACGGAT

Alignment

ORF - retro_tsyr_1134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.68 %
• Parental protein coverage: 70.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTEFWLISAPGEKT-CQQTWEKLHAATTKNNNLAVTCKFNIPDLKVGTLDVLVGLSDELAKLDAFVEGVV
          MTEF.LI.APGEK..CQQTWEKLH.ATTKNNNLAVT.KFNIPDL.VGTL..LVGLSDELAK.DAFVEGV.
Retrocopy MTEFLLIFAPGEKN>CQQTWEKLHVATTKNNNLAVTSKFNIPDLRVGTLNILVGLSDELAKVDAFVEGVI

Parental  KKVAQYMADVLEDSKDKVQENLLANGVDLVTYITRFQWDMAKYPIKQSLKNISEIIAKGVTQIDNDLKSR
          KKVAQYMADVLED.KDK.QE.LLANGVDL..YI.RFQWDMAKYPI.Q.LKNISEIIAK..TQIDN.LKS.
Retrocopy KKVAQYMADVLEDNKDKFQEYLLANGVDLLAYIARFQWDMAKYPIMQVLKNISEIIAKRITQIDNVLKSQ

Parental  ASAYNNLK-GNLQNLERKNAGSLLTRSLAEIVKKDDFVLDSEYLVTLLVVVPKLNHNDWIKQYETLAEMV
          AS..NNLK.G..........G.LLTRSLA.IVKKDDFVLDSEYLVTLLV.VPKL.HN.WIKQYETLAE.V
Retrocopy ASTFNNLK>GTFRTWSERMQG-LLTRSLAGIVKKDDFVLDSEYLVTLLVAVPKLKHNAWIKQYETLAEIV

Parental  VPRSSNVLSEDQDSYLCNVTLFRKAVDDFRHKARENKFIVRDFQYNEEEMKADKEEMNRLSTD
          VPRSS.VLSEDQ.SYLCNVTLF.KAVDDFRHKARENKF.V..FQYNEEEMKADKEEM.R.STD
Retrocopy VPRSSHVLSEDQGSYLCNVTLFSKAVDDFRHKARENKFLVHGFQYNEEEMKADKEEMSRFSTD

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_1134 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
Loxodonta africana	ENSLAFG00000011909	1 retrocopy	retro_lafr_406,
Sarcophilus harrisii	ENSSHAG00000018681	1 retrocopy	retro_shar_89,
Tarsius syrichta	ENSTSYG00000006233	1 retrocopy	retro_tsyr_1134 ,