RetrogeneDB ID: retro_dnov_799

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_108891:6261..7348(-)
• Located in intron of: None

Retrocopy information

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

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_799
ATGAACAGTCAGCTCAACGGCTTCCACGAGGCGTTCATTGAGGAGGGCACATTCCTCTTCACCTCAGAGTCTGTGGGGGA
AGGCCACCCAGATAAGATTTGTGACCAGATCAGTGATGCTGTGCTTGATGCCCACCTTCAGCAGGACCCTGATGCCAAAG
TAGCTTGTGAACTGTTGGCTAAACTGGGAATGATCCTTCTTGCTGGGGAAATTACATCCAGAGCTGCTGTTGCACTATCC
AGAAAGTGGTTCGTGAAACCATTAAACACATTGGCTATGATGATTCTTCCAAAGGTTTTGACTACAAGACCTGTAATGTG
CTGGTGGCCTTGGAACAACAATCACCAGATATTGCTCAAGGCATTCATCTTGATCGGAATGAGGAAGACATTGGTGCAGG
AGACCAGGGTTTGATGTTTGGTTAAGCCACTGATGAAACTGAAGAGTGTATGCCTTTAACCATTGTCTTAGCACACAAGC
TCAATGCCAAACTGGCTGAACTACGCCGCAATGGCACTTTGCCTTGGCTACGCCCAGATTCTAAAACTCAAGTGACAGTG
CAGTACATGCAGGATTGAGGTGCTGTGCTTCCCATCAGAGTCCACACAATTCTGATATCGGTTCAGCATGATGAAGATGT
TTGTCTTGATGAGATGAGGGATGCCCTAAAGGAGAAAGTCATCAAAGCTGTTGTACCTGCAAAATGCCTTGATGAGGATA
CAATCTACCACCTTCAGCCAAGTGGCAGATTTGTTATTGGTGGGCCTCAGAGTGATGCTGGTTTGACTGGCCGGAAGATC
ATTGTGGACACTTATGGTGGTTGGGGAACTCACGGAGGAGGTGCCTTTTCAGGAAAGGATTATACCAAGGTGGACCGTTC
TGCTGCTTATGCTGCTCGTTGGGTGGCAAAATCCCTTGTTAAAGGAGGTTTATGCAGAAGGTTCTTGTTCAGGTCTCTTA
TGCTATTGGAGTTTCTCATCCATTGTCTATCTCCATTTTCCATTATGGCACCTCTCAGAAGAGTGAGAGAGAGCTATTAG
AGATTGTGAAGAAGAATTTTGACCTCCGCCCTGGGGTCATTGTCAGG

Alignment

ORF - retro_dnov_799 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.05 %
• Parental protein coverage: 91.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNGPVDGLCDHSLSEEGAFMFTSESVGEGHPDKICDQISDAVLDAHLRQDPNAKVACETVCKTGMVLLC-
          MN....G.......EEG.F.FTSESVGEGHPDKICDQISDAVLDAHL.QDP.AKVACE...K.GM.LL..
Retrocopy MNSQLNGFHE-AFIEEGTFLFTSESVGEGHPDKICDQISDAVLDAHLQQDPDAKVACELLAKLGMILLA>

Parental  GEITSGAMVDY-QRVVRDTIQHIGYDDSAKGFDFKTCNVLVALEQQSSDIAQCVHLDRNEEDFGAGDQGL
          G.........Y.Q.VVR.TI.HIGYDDS.KGFD.KTCNVLVALEQQS.DIAQ..HLDRNEED.GAGDQGL
Retrocopy GKLHPELLLHY>QKVVRETIKHIGYDDSSKGFDYKTCNVLVALEQQSPDIAQGIHLDRNEEDIGAGDQGL

Parental  MFGYATDETEECMPLTIILAHKLNARMADLRRSGVLPWLRPDSKTQVTVQYMQDNGAVIPLRIHTIVISV
          MFG.ATDETEECMPLTI.LAHKLNA..A.LRR.G.LPWLRPDSKTQVTVQYMQD.GAV.P.R.HTI.ISV
Retrocopy MFG*ATDETEECMPLTIVLAHKLNAKLAELRRNGTLPWLRPDSKTQVTVQYMQD*GAVLPIRVHTILISV

Parental  QHDEDIDLEGMRTALKEQVIRAVVPAKYLDEDTIYHLQPSGRFVIGGPQGDAGVTGRKIIVDTYGGWGAH
          QHDED..L..MR.ALKE.VI.AVVPAK.LDEDTIYHLQPSGRFVIGGPQ.DAG.TGRKIIVDTYGGWG.H
Retrocopy QHDEDVCLDEMRDALKEKVIKAVVPAKCLDEDTIYHLQPSGRFVIGGPQSDAGLTGRKIIVDTYGGWGTH

Parental  GGGAFSGKDYTKVDRSAAYAARWVAKSLVKAGLCRR-VLVQVSYAIGVAEPLSISIFTYGTSRKTERELL
          GGGAFSGKDYTKVDRSAAYAARWVAKSLVK.GLCRR.VLVQVSYAIGV..PLSISIF.YGTS.K.ERELL
Retrocopy GGGAFSGKDYTKVDRSAAYAARWVAKSLVKGGLCRR<VLVQVSYAIGVSHPLSISIFHYGTSQKSERELL

Parental  DIVNKNFDLRPGVIVR
          .IV.KNFDLRPGVIVR
Retrocopy EIVKKNFDLRPGVIVR

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	35.00 RPM	0.58 RPM
SRP012922_cerebellum	33.68 RPM	0.41 RPM
SRP012922_heart	6.26 RPM	0.23 RPM
SRP012922_kidney	15.06 RPM	14.78 RPM
SRP012922_liver	3.10 RPM	1175.60 RPM
SRP012922_lung	25.66 RPM	0.92 RPM
SRP012922_quadricep_muscle	6.40 RPM	0.35 RPM
SRP012922_spleen	32.05 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_799 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,