RetrogeneDB ID: retro_tsyr_2014

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_79317:5827..6854(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSTSYG00000014544
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAT1A
• Ensembl ID: ENSTSYG00000000972
• Aliases: None
• Description: methionine adenosyltransferase I, alpha [Source:HGNC Symbol;Acc:6903]

Sequence

>retro_tsyr_2014
ATGCACGGCCAGCTCAACGGCTTCCACGAGGCGTTCATCGAGGCGGGCACCTTCCTCTTCACCTCCAAGTTCATGGAGGA
AGCCACCCAAATAAGATCTGTGACCAGATCAGCGATCTGTCCTTGATGCCCACCTTCAGCAGGATCCTGATGCCAAATGG
CTTGCGAAACTGTTGCTAAGACCGGAATGATCCTTCTTGCTGGAGAAATTACATCCAGAGCTGCTGTTGACTACCAGAAA
GTGGTTCGTGAAGCCATTCAACACATTGGATATGATGATTCATCCAAAGGGTTTGACTACAAGACTTGTAATGTGTTGGT
GGCCCTGGAGCAGCAGTCACCAGATATTGCCCAAGGTGTTCATCTTGACCAGAATGAAGAAGACATTGGCGCTGGAGACC
AGGGCTTGATGTTTGGCTATACCACTGATGAAACTGAGGAATGTATGCCTTTAACCATTGTCTTGGCACACATGCTCAAT
GTCAAACTGGCAGAACTGCGCCGCAATGGCACTTTGCCTTGGTTACGCCCTGATTCGAAAACTCAAGTGACCGTGCAGTA
TATGCAGGATCGAGGTGCTGTGCTTCCTATTAGAGTCCACACAATTGTTATATCTGTTCAGCATGATGAAGAAGTTTGTC
TCGATGAGATGAGGGATGCCCTAAAGGAAAGGGTCATCAAAGCTGTGGTGCCTGCAAAATATCTCGATGAGGACACAATC
TACCATCTGTAGCCTAGTGGCAGATTTATTATTGGTGGGCCTCAGGGTGATGCTGGTTTGGCCAGAAAATCACTGTGGAC
ACTTATGGCGGCTGGGGAGCTCATAGAGGAGGTGCCTTTTCGGAAAAGGATTATACCAAGGTGGACCTTTTCGCTGCTTA
TGCTGCTCGTTGGGTGGCAAAGTCCCTTGTTAAAGAGGTCTGTGCAGGAGGGTTCTTGTTCAGGTCTCTTATGCTATTGG
AGTTTCTCATCCATTGTCTATCTCCATTTTCCATTATGGTACAGAAGAGTGAGAGAGAGCTATTATG

Alignment

ORF - retro_tsyr_2014 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.36 %
• Parental protein coverage: 97.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MNGPVDGLCDHSLTEEGAFMFTSESV-GEGHPDKICDQISD-AVLDAHLKQDPNAK-VACETVCKTGMVL
          M.G...G.......E.G.F.FTS....G..HP.KICDQISD..VLDAHL.QDP.AK..ACETV.KTGM.L
Retrocopy MHGQLNGFHE-AFIEAGTFLFTSKFM<GGSHPNKICDQISD<SVLDAHLQQDPDAK<MACETVAKTGMIL

Parental  LCGEITSVAMVDYQRVVRDTIKHIGYDDSAKGFDFKTCNVLVALEQQSPDIAQCVHLDRNEEDVGAGDQG
          L.GEITS.A.VDYQ.VVR..I.HIGYDDS.KGFD.KTCNVLVALEQQSPDIAQ.VHLD.NEED.GAGDQG
Retrocopy LAGEITSRAAVDYQKVVREAIQHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGVHLDQNEEDIGAGDQG

Parental  LMFGYATDETEECMPLTIILAHKLNARMADLRRSGVLPWLRPDSKTHVTVQYTQDNGAVIPVRIHTIVIS
          LMFGY.TDETEECMPLTI.LAH.LN...A.LRR.G.LPWLRPDSKT.VTVQY.QD.GAV.P.R.HTIVIS
Retrocopy LMFGYTTDETEECMPLTIVLAHMLNVKLAELRRNGTLPWLRPDSKTQVTVQYMQDRGAVLPIRVHTIVIS

Parental  VQHNEDITLEEMRGALKEQVIRAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRK-IIVDTYGGWG
          VQH.E...L.EMR.ALKE.VI.AVVPAKYLDEDTIYHL.PSGRF.IGGPQGDAG...RK.I.VDTYGGWG
Retrocopy VQHDEEVCLDEMRDALKERVIKAVVPAKYLDEDTIYHL*PSGRFIIGGPQGDAGL-ARK<ITVDTYGGWG

Parental  AHGGGAFSGKDYTKVDRSAAYAARWVAKSLVK-AGLCRRVLVQFPYAIGVAEPLSISLFTYGTSKTYREL
          AH.GGAFS.KDYTKVD..AAYAARWVAKSLVK..GLCRRVLVQ..YAIGV..PLSIS.F.YGT....R..
Retrocopy AHRGGAFSEKDYTKVDLFAAYAARWVAKSLVK<RGLCRRVLVQVSYAIGVSHPLSISIFHYGTEE*ERAI

Parental  L
          .
Retrocopy M

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_2014 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003326	2 retrocopies	retro_dnov_799, retro_dnov_885,
Tarsius syrichta	ENSTSYG00000000972	1 retrocopy	retro_tsyr_2014 ,