RetrogeneDB ID: retro_dnov_885

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_11784:14121..15306(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000012291
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAT1A
• Ensembl ID: ENSDNOG00000003326
• Aliases: None
• Description: methionine adenosyltransferase I, alpha [Source:HGNC Symbol;Acc:6903]

Sequence

>retro_dnov_885
ATGAACAGTCAGCTCAACGGCTTCCACGAGGCGTTCATTGAGGAGGGCACATTCCTCTTCACCTCAGAGTCTGTGGGGGA
AGGCCACCCAGATAAGATTTGTGACCAGATCAGTGATGCTGTGCTTGATGCCCACCTTCAGCAGGACCCTGATGCCAAAG
TAGCTTGTGAAACTGTTGCTAAAACTGGAATGATCCTTCTTGCTGGGGAAATTACATCCAGAGCTGCTGTTGACTACCAG
AAAGTGGTTCGTGAAACCATTAAACACATTGGCTATGATGATTCTTCCAAAGGGTTTGACTACAAGACCTGTAATGTGCT
GGTGGCCTTGGAACAACAATCACCAGATATTGCTCAAGGCATTCATCTTGATCGGAATGAGGAAGACATTGGTGCAGGAG
ACCAGGGTTTGATGTTTGGTTAAGCCACTGATGAAACTGAAGAGTGTATGCCTTTAACCATTGTCTTAGCACACAAGCTC
AATGCCAAACTGGCTGAACTACGCCGCAATGGCACTTTGCCTTGGCTACGCCCAGATTCTAAAACTCAAGTGACAGTGCA
GTACATGCAGGATTGAGGTGCTGTGCTTCCCATCAGAGTCCACACAATTCTGATATCGGTTCAGCATGATGAAGATGTTT
GTCTTGATGAGATGAGGGATGCCCTAAAGGAGAAAGTCATCAAAGCTGTTGTACCTGCAAAATGCCTTGATGAGGATACA
ATCTACCACCTTCAGCCAAGTGGCAGATTTGTTATTGGTGGGCCTCAGAGTGATGCTGGTTTGACTGGCCGGAAGATCAT
TGTGGACACTTATGGTGGTTGGGGAACTCACGGAGGAGGTGCCTTTTCAGGAAAGGATTATACCAAGGTGGACCGTTCTG
CTGCTTATGCTGCTCGTTGGGTGGCAAAATCCCTTGTTAAAGGAGGTTTATGCAGAAGGGTTCTTGTTCAGGTCTCTTAT
GCTATTGGAGTTTCTCATCCATTGTCTATCTCCATTTTCCATTATGGCACCTCTCAGAAGAGTGAGAGAGAGCTATTAGA
GATCGTGAAGAAGAATTTTGACCTCCGCCCTGGGGTCATTGTCAGGGATCTGGATCTGAAGAAGCCAATTTATCAGAGGA
CTGCAGCCTATGGCCACTTTGGTAGGGACAGCTTCCCATGGGAAGTGCCCAAAAAGCTTAAATAT

Alignment

ORF - retro_dnov_885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGPVDGLCDHSLSEEGAFMFTSESVGEGHPDKICDQISDAVLDAHLRQDPNAKVACETVCKTGMVLLCG
          MN....G.......EEG.F.FTSESVGEGHPDKICDQISDAVLDAHL.QDP.AKVACETV.KTGM.LL.G
Retrocopy MNSQLNGFHE-AFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACETVAKTGMILLAG

Parental  EITSGAMVDYQRVVRDTIQHIGYDDSAKGFDFKTCNVLVALEQQSSDIAQCVHLDRNEEDFGAGDQGLMF
          EITS.A.VDYQ.VVR.TI.HIGYDDS.KGFD.KTCNVLVALEQQS.DIAQ..HLDRNEED.GAGDQGLMF
Retrocopy EITSRAAVDYQKVVRETIKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGIHLDRNEEDIGAGDQGLMF

Parental  GYATDETEECMPLTIILAHKLNARMADLRRSGVLPWLRPDSKTQVTVQYMQDNGAVIPLRIHTIVISVQH
          G.ATDETEECMPLTI.LAHKLNA..A.LRR.G.LPWLRPDSKTQVTVQYMQD.GAV.P.R.HTI.ISVQH
Retrocopy G*ATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQD*GAVLPIRVHTILISVQH

Parental  DEDIDLEGMRTALKEQVIRAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAHGG
          DED..L..MR.ALKE.VI.AVVPAK.LDEDTIYHLQPSGRFVIGGPQ.DAG.TGRKIIVDTYGGWG.HGG
Retrocopy DEDVCLDEMRDALKEKVIKAVVPAKCLDEDTIYHLQPSGRFVIGGPQSDAGLTGRKIIVDTYGGWGTHGG

Parental  GAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRRVLVQVSYAIGVAEPLSISIFTYGTSRKTERELLDIV
          GAFSGKDYTKVDRSAAYAARWVAKSLVK.GLCRRVLVQVSYAIGV..PLSISIF.YGTS.K.ERELL.IV
Retrocopy GAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRRVLVQVSYAIGVSHPLSISIFHYGTSQKSERELLEIV

Parental  NKNFDLRPGVIVRDLDLKKPIYQKTACYGHFGRSEFQ-EVPKRLVF
          .KNFDLRPGVIVRDLDLKKPIYQ.TA.YGHFGR..F..EVPK.L..
Retrocopy KKNFDLRPGVIVRDLDLKKPIYQRTAAYGHFGRDSFPWEVPKKLKY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012922_ascending_colon	45.51 RPM	0.58 RPM
SRP012922_cerebellum	44.13 RPM	0.41 RPM
SRP012922_heart	12.99 RPM	0.23 RPM
SRP012922_kidney	39.70 RPM	14.78 RPM
SRP012922_liver	8.36 RPM	1175.60 RPM
SRP012922_lung	49.94 RPM	0.92 RPM
SRP012922_quadricep_muscle	15.75 RPM	0.35 RPM
SRP012922_spleen	54.14 RPM	0.11 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_885 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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,