RetrogeneDB ID: retro_tsyr_1998

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_77290:1021..1560(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2T
• Ensembl ID: ENSTSYG00000001704
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2T (putative) [Source:HGNC Symbol;Acc:25009]

Sequence

>retro_tsyr_1998
CAGAGAGTTTCCCAACTGAAGAAAGAGCTGCACATGTTAGCCACAGAGGTACCCTCACACATCACATGCTGGCAAGTAAA
GACCAAATGGATGATCTGCGAGCTCAGATATTGGGTGGAGACAACACACCTTATGAGAAAGGTATTTTCAAGCTGGAAGT
TATCATTCCTGAGAGGTACCCATTTGAACTGCCTCAGATTCAATTTCTCACTCCAGTTTATCATCCAAACATTGATTCAG
GTGGAAGGATCTGTTTATATGTTCTCAAATTTCCACCAAAAGGTGCCTGGAGACCATTCATAACATTGCAACTGTGTTGA
CCTCTATTCAACTGCTCATATCAGAACCCCACCCTGACGACCCACTCATGGCTGATATATCCTCAGAATTTAAATATAAT
AAGCCAGTCTTCCTTTAAAAAATGCCAGGCAGTGGACAGAGAAGCCTGCAAGACAAAAGTTGATGAGGAGAAGTGCTTGA
TACTCTACCAGAGGCTGCTGATGCCAAAATACACAGCTCACACAGAAAGGAAAGCCGGA

Alignment

ORF - retro_tsyr_1998 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.01 %
• Parental protein coverage: 92.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  QRASRLKKELHMLATEPPPGITCWQ-DKDQMDDLRAQILGGTNTPYEKGVFKLEVIIPERYPFEPPQIRF
          QR.S.LKKELHMLATE.P..ITCWQ..KDQMDDLRAQILGG.NTPYEKG.FKLEVIIPERYPFE.PQI.F
Retrocopy QRVSQLKKELHMLATEVPSHITCWQ<SKDQMDDLRAQILGGDNTPYEKGIFKLEVIIPERYPFELPQIQF

Parental  LTPIYHPNIDSAGRICLDVLKLPPKGAWRPSL-NIATVLTSIQLLMSEPNPDDPLMADISSEFKYNKPVF
          LTP.YHPNIDS.GRICL.VLK.PPKGAWRP...NIATVLTSIQLL.SEP.PDDPLMADISSEFKYNKPVF
Retrocopy LTPVYHPNIDSGGRICLYVLKFPPKGAWRPFI<NIATVLTSIQLLISEPHPDDPLMADISSEFKYNKPVF

Parental  L-KNARQWTEKHARQRADEE-EMLDNLPEAAVSEIHSS-TQK-RKAG
          L.K..............DEE.E.LD.LPEAA...IHSS.TQK.RKAG
Retrocopy L>KKCQAVDREACKTKVDEE<EVLDTLPEAADAKIHSS<TQK<RKAG

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_1998 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 4 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000010249	3 retrocopies	retro_ocun_402, retro_ocun_403, retro_ocun_910,
Otolemur garnettii	ENSOGAG00000029029	1 retrocopy	retro_ogar_1392,
Tarsius syrichta	ENSTSYG00000001704	4 retrocopies	retro_tsyr_1998 , retro_tsyr_208, retro_tsyr_379, retro_tsyr_991,
Tarsius syrichta	ENSTSYG00000008800	5 retrocopies	retro_tsyr_1476, retro_tsyr_1754, retro_tsyr_207, retro_tsyr_348, retro_tsyr_5,