RetrogeneDB ID: retro_tsyr_1560

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_49027:1704..2542(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC20
• Ensembl ID: ENSTSYG00000012703
• Aliases: None
• Description: cell division cycle 20 [Source:HGNC Symbol;Acc:1723]

Sequence

>retro_tsyr_1560
ATGGCGCAGTTCGTGTTGGAGAGTGACCTGCACTCGCTTCTGCAGCTGGACGCATTCATCCCCAATGCGCTCCCCGCGCG
CTGGCAGCGCAAAGCCAAGGAGGCCGCAGGCCCGGCCCCCTCGCCCATGCGGGCCGCCAACTGATCTCACAGCGCCAGCA
GGACTCCGAGCCGAACTCCCGGCAAATCCAGCTCCAAAGTTCAGACCACTCCTAGCAAGCCTGGCGGCGACCGCTATATC
CCCCAGCGCAGCCCTTCTCAGATGGAGGTGGCCAGCTTCCTTCTAAGCAAGGAGAATCAGCCGGAGGACAACCAGACGCC
CATCAAGAAGGAACATCAGAAAGCCTGGGCTTTGAATTTTGATGTGGAGGAAGCCAAGATCCTTTGGCTCAGTGAAAAAC
CACAAAATGCCCCCAGAGGGTTACCAGAACAGACTGAAAGTACTCTATAGCCAGAAGGCCACACCTGGCTTCAGCCGAAA
GACCTGCCGTTACATTCCCTCCCTGCCAGACCGGATCCTGGAGGCCTCTGAAATCCGAAATGACTACTACTTGAACCTTG
TGGGTTGGAGCTCTGGGAACGTACTGGCTGTGGCACTGGATAACAGCGTGTACCTGTGGAGTGCTGGCTCTGGTGACATT
CTTCAGTTGTTGCAAATGGAGCAGCCTGGGGAATATGGATCCGCTGTGACCTGGATCAAAGAGGACAACTACTTGGCTGT
GGGCACCAGCAGTGCTGAGGTGCAGCTATGGGATGTGCCACAGCAGAAACGGCTTCGAAATATGACCAGTCACTCTGCTC
GAGTGGGTTCCCTAAGTAGGAACAGCTATATCCTTTCC

Alignment

ORF - retro_tsyr_1560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.17 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQFVFESDLHSLLQLDAPIPNAPPARWQRKAKEAAGPAPSPMRAANRSHSAGRTPGRTPGKSSSKVQTT
          MAQFV.ESDLHSLLQLDA.IPNA.PARWQRKAKEAAGPAPSPMRAAN.SHSA.RTP.RTPGKSSSKVQTT
Retrocopy MAQFVLESDLHSLLQLDAFIPNALPARWQRKAKEAAGPAPSPMRAAN*SHSASRTPSRTPGKSSSKVQTT

Parental  PSKPGGDRYIPHRSASQMEVASFLLSKENQPEDNQTPTKKEHQKAWALNLNGFDVEEAKILRLSGKPQNA
          PSKPGGDRYIP.RS.SQMEVASFLLSKENQPEDNQTP.KKEHQKAWALN...FDVEEAKIL.LS.KPQNA
Retrocopy PSKPGGDRYIPQRSPSQMEVASFLLSKENQPEDNQTPIKKEHQKAWALN---FDVEEAKILWLSEKPQNA

Parental  P-EGYQNRLKVLYSQKATPGSSRKTCRYIPSLPDRILDAPEIRNDYYLNLVDWSSGNVLAVALDNSVYLW
          P.EGYQNRLKVLYSQKATPG.SRKTCRYIPSLPDRIL.A.EIRNDYYLNLV.WSSGNVLAVALDNSVYLW
Retrocopy P>EGYQNRLKVLYSQKATPGFSRKTCRYIPSLPDRILEASEIRNDYYLNLVGWSSGNVLAVALDNSVYLW

Parental  SAGSGDILQLLQMEQPGEYVSSVAWIKEGNYLAVGTSSAEVQLWDVQQQKRLRNMTSHSARVGSLSWNSY
          SAGSGDILQLLQMEQPGEY.S.V.WIKE.NYLAVGTSSAEVQLWDV.QQKRLRNMTSHSARVGSLS.NSY
Retrocopy SAGSGDILQLLQMEQPGEYGSAVTWIKEDNYLAVGTSSAEVQLWDVPQQKRLRNMTSHSARVGSLSRNSY

Parental  ILS
          ILS
Retrocopy ILS

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_1560 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006680	2 retrocopies	retro_chof_2172, retro_chof_2286,
Callithrix jacchus	ENSCJAG00000003414	1 retrocopy	retro_cjac_1608,
Homo sapiens	ENSG00000117399	1 retrocopy	retro_hsap_4187,
Gorilla gorilla	ENSGGOG00000010419	1 retrocopy	retro_ggor_96,
Mus musculus	ENSMUSG00000006398	1 retrocopy	retro_mmus_1536,
Nomascus leucogenys	ENSNLEG00000013419	1 retrocopy	retro_nleu_2847,
Pongo abelii	ENSPPYG00000001448	1 retrocopy	retro_pabe_3428,
Pan troglodytes	ENSPTRG00000000634	1 retrocopy	retro_ptro_2843,
Tarsius syrichta	ENSTSYG00000012703	3 retrocopies	retro_tsyr_1560 , retro_tsyr_442, retro_tsyr_938,
Tursiops truncatus	ENSTTRG00000010813	1 retrocopy	retro_ttru_1309,