RetrogeneDB ID: retro_tsyr_1531

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_481227:0..725(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000004335
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTERFD2
• Ensembl ID: ENSTSYG00000012283
• Aliases: None
• Description: MTERF domain containing 2 [Source:HGNC Symbol;Acc:28785]

Sequence

>retro_tsyr_1531
GTCCTTGACTGGCACCAACTGATCCCCCTCACCTGGGCCTGTGTGGCCAGGCACACTTCTCTTGGAGAACAGAAAAGGAT
GGCTGCTTCCTTGTTGCGTAAACTGACTACAACTTCCAATAGAGGGAGATTTGAGGAGTTATCTTATGTTGGATCCAATA
AATATGTGCAGGAACCAGAGTGTAGGATGAATCTTGTTCAATGTCTCCATGAGAAGCAGAGATCCACTCTTATGGATCAA
GAGGCCTTGGAGCTAGAAAATATCATCAGTTCCCTCCTGGATATGGGTTTCAGTGATGCTCATATTAATGAATTGCTCGG
TGTACAACCAGGTGCTAACCTTCAACAGATGCTGGACATCATTTCAGAATTTATACTCTTGGGTAAGCATCCAGAGCCCG
TGTATCTGGCCCTGATGAAAAGTCCCCAGTTATTGAAAATGTGTTTAATGCAAATGAAGAAGCGCTCCAGTTATGTGCAA
AAGCTTGGGCTTAAGAAGGGAAACTAAAGAGGATGCTTCAGTGGTGCCCCGAAATTTTTGATATGCATCAACAGAACATT
GAGGACATTGTCAGGGTCCTCAAGGAGAAGTGCCTTTTCACAGTACAGCAAGTCACGGAGATTTTCCACAGATGCCCCTC
TGTTATTCAGGAGAATCCAGGTGAATTGGAATACAGATTCCAGTATGCATATTTTAGGATGGGAATTAAGCATCCAGACA
TGGTA

Alignment

ORF - retro_tsyr_1531 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.48 %
• Parental protein coverage: 71.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VLDWHRLISLTWACMARQTTSLGEQKRMTASLLRKLTTASNRGSLEELSYVGSNKYVQEPECRMNLVQCL
          VLDWH.LI.LTWAC.AR.T.SLGEQKRM.ASLLRKLTT.SNRG..EELSYVGSNKYVQEPECRMNLVQCL
Retrocopy VLDWHQLIPLTWACVARHT-SLGEQKRMAASLLRKLTTTSNRGRFEELSYVGSNKYVQEPECRMNLVQCL

Parental  REKQRSTPMDQEALELENIISSLLDMGFSDAHINELLSVQPGANLQQMVDIISEFILLGLNPEPVYVALK
          .EKQRST.MDQEALELENIISSLLDMGFSDAHINELL.VQPGANLQQM.DIISEFILLG..PEPVY.AL.
Retrocopy HEKQRSTLMDQEALELENIISSLLDMGFSDAHINELLGVQPGANLQQMLDIISEFILLGKHPEPVYLALM

Parental  KNPQLLKMSVMQMKKRSRYLRKLGLE-EGKLKRVLQCCPEIFTMHQQNIEDIVRVLKEKCLFTVQQVTEI
          K.PQLLKM..MQMKKRS.Y..KLGL..EGKLKR.LQ.CPEIF.MHQQNIEDIVRVLKEKCLFTVQQVTEI
Retrocopy KSPQLLKMCLMQMKKRSSYVQKLGLK<EGKLKRMLQWCPEIFDMHQQNIEDIVRVLKEKCLFTVQQVTEI

Parental  LHRCPSVLHENPDELEYKFQYAYFRMGIKHPDMV
          .HRCPSV..ENP.ELEY.FQYAYFRMGIKHPDMV
Retrocopy FHRCPSVIQENPGELEYRFQYAYFRMGIKHPDMV

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_1531 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Tarsius syrichta	ENSTSYG00000012283	3 retrocopies	retro_tsyr_1286, retro_tsyr_1531 , retro_tsyr_230,