RetrogeneDB ID: retro_tsyr_2074

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_86908:5136..5645(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GTF2E2
• Ensembl ID: ENSTSYG00000013143
• Aliases: None
• Description: general transcription factor IIE, polypeptide 2, beta 34kDa [Source:HGNC Symbol;Acc:4651]

Sequence

>retro_tsyr_2074
AAGGCATTAGTCAACAATCCCCAAATTGAAGTAATCGATGGGAAGAATGCTTTTAAGCCCAAGTACCACGTGAAAGATGA
GAAATCCCTCCTCAGACTCCTAGATCAGCATGACCAGCGAGGATTAGGAGGAATTCTTTTCGAAGACATAGAAGAACTGC
CCAATTCCCAGAAAGCTGTCAAGGCTTTGGGGGACCAGATACTATCTGTAAATCGTCCTGATAAGAAGAAAATACTTTTC
TTCAATGATAAGAGCTGCCAGTTTTCTGTGGATGAAGAATTTCAGAAGCTGTGGAGGAGTGTCACTGTGGATTCGATGAA
TGAGGAGAAAATTGAAGAATATCTGAAGCGACAGGATATTTCTTCTATGCAGGAGTCTGAACCAAAGAAAGTGACCCCTA
TTCAGAGAAGGAAAAAAGCCTGCTTCCCAGAAAAGAGTGCCGCCTTAAGACTCATAACGAACACTTGGCTGGAATGCTGA
AGGATTACTCCGACATTACTCCTGGCAAA

Alignment

ORF - retro_tsyr_2074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.37 %
• Parental protein coverage: 58.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EALVNNPKIEVVDGKYAFKPKYNVKDKKSLLRLLDQHDQRGLGGILLEDIEEGLPNSQKAVKALGDQILF
          .ALVNNP.IEV.DGK.AFKPKY.VKD.KSLLRLLDQHDQRGLGGIL.EDIEE.LPNSQKAVKALGDQIL.
Retrocopy KALVNNPQIEVIDGKNAFKPKYHVKDEKSLLRLLDQHDQRGLGGILFEDIEE-LPNSQKAVKALGDQILS

Parental  VSRPDKKKILFFNDKSCQFSVDEEFQKLWRSVTVDSMDEEKIEEYLKRQGISSMQESGPKKVAPIQRR-K
          V.RPDKKKILFFNDKSCQFSVDEEFQKLWRSVTVDSM.EEKIEEYLKRQ.ISSMQES.PKKV.PIQRR.K
Retrocopy VNRPDKKKILFFNDKSCQFSVDEEFQKLWRSVTVDSMNEEKIEEYLKRQDISSMQESEPKKVTPIQRR>K

Parental  KPASQKK-RRFKTHNEHLAGVLKDYSDITPGK
          KPASQK...R.KTHNEHLAG.LKDYSDITPGK
Retrocopy KPASQKR>CRLKTHNEHLAGMLKDYSDITPGK

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_2074 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005031	1 retrocopy	retro_dnov_2321,
Macropus eugenii	ENSMEUG00000010541	1 retrocopy	retro_meug_546,
Myotis lucifugus	ENSMLUG00000007814	1 retrocopy	retro_mluc_2029,
Sorex araneus	ENSSARG00000007758	2 retrocopies	retro_sara_376, retro_sara_569,
Sus scrofa	ENSSSCG00000015845	1 retrocopy	retro_sscr_878,
Tarsius syrichta	ENSTSYG00000013143	1 retrocopy	retro_tsyr_2074 ,
Tursiops truncatus	ENSTTRG00000012464	1 retrocopy	retro_ttru_859,