RetrogeneDB ID: retro_tsyr_746

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_18731:8170..9223(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSTSYG00000006777
• Aliases: None
• Description: None

Sequence

>retro_tsyr_746
GACGAGGAGCAGCAGGAGCAAACTATCAATCTGGTTGTGACCAAGTATAAGATGGGGGACGACATAGCCAAACGGGTACT
TCGGTCCTTGGTAGAAGCATCCAGCTCAGGTGTGTCGGTACTGAGCCTGTGTGAGAAAGGTGATGCCATGATTATGGAAG
AGACAGGGAAAATCTTCTAGAAAGAAAAGGAAATGAAGAAAGGTATTGCTTTTCCCACCAGCATTTCAGTAAATAACTGT
GTATGTCACTTCTCCCCTTTGAAGAGCGACCAGGACTATATTCTCAAGGAAGGTGACTTGGTAAAAATTGACCTTGGAGT
CCACATGGATGGCTTCATCACTAATGTAGCTCACACATTCGTGGTCGGTGTGGCTCAGGGGACCCAGGTAACAGGGCGGA
AAGCAGATGTCATTAAGGCAGCTCACCTTTGTGCTGAAGCTGCCCTCCGCTTGGTCAAACCTGGAAACCAGAACATACAA
GTGACAGAATCCTGGAACAAAGTTGCTCACTCATTTAATTGCACGCCAACAGAAGGTATGCTGTCACACCAGCTGAAGCA
GCATGTCACTGATGGAGAGAAGACCATTATCCAGAATCCCACAGACCAGCAGAAGAAGGACCACGAAAAGGCTGAATTTG
AGGTACATGAAGTAGATGCTGTGGATGTCCTGGTCAGCTCAGGAGAGGGCAAGACCAAGGATGCAGGGCAGAGGACTACT
ATTTACAAACGAGACCCCACTAAACAGTATGGACTGAAAATGAAAACTTCCAGTGCCTTCTTCAGTGAGGTGGAAAGGTG
TTTTGATGCCATGTCATTTACTTTAAGGGCATTTGACGATGAGAAGAAGGCTTGGATGGGTGTGGTGGAGTGCACCAAAC
ATGAACTGTTGCAACCATTTAATGTTCTCTATGAGAAGGAAGGTGAATTTGTAACCCAGTTTAAATTTACAGTTCTGCTC
ATGCCCAACGACCCCATGCGGATAACCAGTGGTCCCTCTGAGCCTGACTCTACAAGTTTGAGATGGAAGGTCCAGGATGC
AGAGCTGAACGCC

Alignment

ORF - retro_tsyr_746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.41 %
• Parental protein coverage: 94.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EDEQQEQTIAEDLVVTKYKMGGDIANRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIFKKEKEMKKG
          ..EQQEQTI...LVVTKYKMG.DIA.RVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIF.KEKEMKKG
Retrocopy DEEQQEQTI--NLVVTKYKMGDDIAKRVLRSLVEASSSGVSVLSLCEKGDAMIMEETGKIF*KEKEMKKG

Parental  IAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHVDGFIANVAHTFVVGVAQGTQVTGRRADVI
          IAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVH.DGFI.NVAHTFVVGVAQGTQVTGR.ADVI
Retrocopy IAFPTSISVNNCVCHFSPLKSDQDYILKEGDLVKIDLGVHMDGFITNVAHTFVVGVAQGTQVTGRKADVI

Parental  KAAHLCAEAALRLVKPGNQNTQVTEAWNKVAHSFNCMLSHQLKQHVIDGEKTIIQNPTDQQKKDHEKAEF
          KAAHLCAEAALRLVKPGNQN.QVTE.WNKVAHSFNC........H......T.......Q...D..K...
Retrocopy KAAHLCAEAALRLVKPGNQNIQVTESWNKVAHSFNCTPTEGMLSHQLKQHVTDGEKTIIQNPTDQQKKDH

Parental  E--VHEVYAVD---VLVSSGEGKAKDAGQRTTIYKRDPSKQYGLKMKTSRAFFSEVERRFDAMPFTLRAF
          E....EV..VD...VLVSSGEGK.KDAGQRTTIYKRDP.KQYGLKMKTS.AFFSEVER.FDAM.FTLRAF
Retrocopy EKAEFEVHEVDAVDVLVSSGEGKTKDAGQRTTIYKRDPTKQYGLKMKTSSAFFSEVERCFDAMSFTLRAF

Parental  DDEKKARMGVVECAKHELLQPFNVLYEKEGEFVAQFKFTVLLMPNGPMRITSGPFEPE-LYKSEME-VQD
          DDEKKA.MGVVEC.KHELLQPFNVLYEKEGEFV.QFKFTVLLMPN.PMRITSGP.EP..LYK.EME.VQD
Retrocopy DDEKKAWMGVVECTKHELLQPFNVLYEKEGEFVTQFKFTVLLMPNDPMRITSGPSEPD<LYKFEME>VQD

Parental  AELKA
          AEL.A
Retrocopy AELNA

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_746 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007181	2 retrocopies	retro_chof_1089, retro_chof_1847,
Homo sapiens	ENSG00000170515	6 retrocopies	retro_hsap_1930, retro_hsap_2413, retro_hsap_2868, retro_hsap_3646, retro_hsap_4191, retro_hsap_4895,
Macaca mulatta	ENSMMUG00000002164	2 retrocopies	retro_mmul_1168, retro_mmul_2631,
Mus musculus	ENSMUSG00000025364	1 retrocopy	retro_mmus_2803,
Oryctolagus cuniculus	ENSOCUG00000017342	1 retrocopy	retro_ocun_1733,
Sus scrofa	ENSSSCG00000000377	1 retrocopy	retro_sscr_338,
Sus scrofa	ENSSSCG00000022666	2 retrocopies	retro_sscr_1143, retro_sscr_337,
Tarsius syrichta	ENSTSYG00000006777	1 retrocopy	retro_tsyr_746 ,
Vicugna pacos	ENSVPAG00000009523	1 retrocopy	retro_vpac_2,