RetrogeneDB ID: retro_tsyr_562

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_140118:3303..4176(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3M2
• Ensembl ID: ENSTSYG00000005974
• Aliases: None
• Description: adaptor-related protein complex 3, mu 2 subunit [Source:HGNC Symbol;Acc:570]

Sequence

>retro_tsyr_562
AACATCCTGAAAGAACTCATAAAGCCTTTCACTATCCTTGGAACAGTTGTCAACACCATCATGGGAAGCACCAATGTGGG
TGACCAACTTCCCACTGGACAGCTGTCAGTGGTGCCTTGGCGATGGACTGGGGTGAAATATACCAACAATGAGACCTATT
TTGATGTGATTGAAGAGATTGATGCCAACATTGATAAATTAGTTTCTACAATTACTGCTGAGTTCCAGGGGGTGATTGAT
ACCTATGACAAGCTGACTGGAATGCCAGAACTTACACTTTCCTTCATGAAGCCCAGGTTGTTGGATGACATTAGCTTGCA
TCCTTTTGTTCATTTCAAGCACTGGGAATCTGAGCAGATCCTCTCCTTCATCCCTCCTGTTGGAAACTTCCACCTGCTCT
ATTACCATGTCAGTGCACAGAATCTGGTTGCAATTCCATTGTATGTCAAACATAATATCAGTTTCCAGGATAGTAGTTCA
CTTGGATACTTTGAAATAACAGTGGGATCCACGTAAACTATGGGGAAGACCATAGAGGGAGTGACTGTCACCAGCCAGAT
GCCCAAAGGAGTCCTGAACATGAGTCTTGCTCCATCTCAGGGGATGCACACGTTTGACCCAGTTACAAAGATGCTCTCTT
GCTATATGAGAAAAATAAATCCCCAAAAGCTACCGAGTTTGAAGGGGACCATGAGTCTTTAGGCTGGAGCTTCCAAACTA
AATGAAAACTCCACAATTAATCTGCAGTTTAAGATCTAGCAGCTGGCCATTTCTGGACTCAAAGTGAATCGTCTGGATAT
GTATGGAGAAAAGTACAAATCCTTCAAGGACATAAAATATATGATCAAAGCTGAAAAGTTCCAAGTTCGAACC

Alignment

ORF - retro_tsyr_562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.54 %
• Parental protein coverage: 69.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NILKELIKPPTILRTVVNTITGSTNVGDQLPTGQLSVVPWRRTGVKYTNNEAYFDVIEEIDAIIDKSGST
          NILKELIKP.TIL.TVVNTI.GSTNVGDQLPTGQLSVVPWR.TGVKYTNNE.YFDVIEEIDA.IDK..ST
Retrocopy NILKELIKPFTILGTVVNTIMGSTNVGDQLPTGQLSVVPWRWTGVKYTNNETYFDVIEEIDANIDKLVST

Parental  ITAEIQGVIDACVKLTGMPDLTLSFMNPRLLDDVSFHPCVRFKRWESERILSFIPPDGNFRLLSYHVSAQ
          ITAE.QGVID...KLTGMP.LTLSFM.PRLLDD.S.HP.V.FK.WESE.ILSFIPP.GNF.LL.YHVSAQ
Retrocopy ITAEFQGVIDTYDKLTGMPELTLSFMKPRLLDDISLHPFVHFKHWESEQILSFIPPVGNFHLLYYHVSAQ

Parental  NLVAIPVYVKHNISFRDSSSLGRFEITVGPKQTMGKTIEGVIVTSQMPKGVLNMSLTPSQGTHTFDPVTK
          NLVAIP.YVKHNISF.DSSSLG.FEITVG...TMGKTIEGV.VTSQMPKGVLNMSL.PSQG.HTFDPVTK
Retrocopy NLVAIPLYVKHNISFQDSSSLGYFEITVGST*TMGKTIEGVTVTSQMPKGVLNMSLAPSQGMHTFDPVTK

Parental  MLSWDIGKINPQKLPSLKGTMSLQAGASKPDENPTINLQFKIQQLAISGLKVNRLDMYGEKYKPFKGIKY
          MLS....KINPQKLPSLKGTMSL.AGASK..EN.TINLQFKI.QLAISGLKVNRLDMYGEKYK.FK.IKY
Retrocopy MLSCYMRKINPQKLPSLKGTMSL*AGASKLNENSTINLQFKI*QLAISGLKVNRLDMYGEKYKSFKDIKY

Parental  MTKAGKFQVRT
          M.KA.KFQVRT
Retrocopy MIKAEKFQVRT

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_562 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013497	1 retrocopy	retro_meug_2142,
Tarsius syrichta	ENSTSYG00000005974	1 retrocopy	retro_tsyr_562 ,
Tarsius syrichta	ENSTSYG00000006101	1 retrocopy	retro_tsyr_1873,