RetrogeneDB ID: retro_mdom_1074

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:524295716..524297260(+)
• Located in intron of: ENSMODG00000029587

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATIC
• Ensembl ID: ENSMODG00000015612
• Aliases: None
• Description: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase [Source:HGNC Symbol;Acc:794]

Sequence

>retro_mdom_1074
GGGGATCTTGCATGCAACTCTGCAGAAGATCAACCTGATGTGGCCAGACTTGATTTCAGTCTTATAAGAATAGTTGTTTG
TAATCTGTATCCCTTCATGAAAACTGTGGCTCCTTCAAATGTAACTGTTGAGGAAGCTGTTGAACAAATTGATATTGGTG
GAGTAACTCTACTCAGAGATGCTACAAAAAATCCTGCTCGAGTGACAGTAGTGTGTGAACCAGGAGATTATGAAGTGGTG
GATACTGAGATGCTGAACTCTGATACTAAAGATACTACTATGGAGACTCGACGGCAGCTTGCATCAAAGGCCTTTACTCT
TACTGCTCAGAATGATCAAGCAATATCAGCTTATTTCAGAAAGGAATCCAGTAAAGGAATAGCTCAGATTCCTTTAAGAT
ATGGAATGATCCCTCGCCAAAAACCTGCACGGTTATATCCAGTGAAGCCCAAACTTCCTCTTACAGTTCTGAATGGATCC
CCTGGGTTTATAAACCTGTGTGATGCCTTGAATGCCTGGCAGTTGGTAAAAGAACTCAGAGAAGCTTCAAGTATTTCAGC
AGCTACCTCCTTCAAGGTGTCAGTCCAGCAGGTGCTGCTATTGGAGTACCACTTGGGGAGGAAGAGCCTGAAGTTTGCAT
GGTTCATGATCTCTACAAGAGCCTTACTCCATTGTCAACTGGACATGGAAGAGCAAGAGGAGCTGACAGAATGTCATCAT
TTGGTGATTTTATTGCTGTTTCTGATGTCTGTGACATCACTACTGCTAAAATTACCTCCAGAGAGGTATCTGATGGTATT
ATTGCACCAGGATATGAAGAGGAAGCCTTGAAGATTCTTTCCAAAAAGAAAAAATGGAAGTTACTGTGTACTGCAGATGG
ACAAACCAGAAGAAGATGAAATTCGTCCTCTCTTTGGATTACATCTAAGTCAGAAGAGGAATAATGGTGTTATTGACAAG
TCATTATTTAACAATATTGTGACAAAGCATAAAGATTTGCCTGAGCCTGCTATTAGAGACCTCATCGTAGCTACTATTGC
TGTCAAATACACGCAGTCCAATTCAGCGTGCCATGCTAAGAACGGTCAGGTAATTGGTGTTGGAGCAGGTCAGCAATCCT
GAATACACTGTACTCGGCTTGCAGGAGATAAGGCAAATAATTGGTGGCTTAGACATCATCCTCGAGTGCTTTCAATGAAA
TTTAAAGCTGGAGTAAAGAGAGCAGAAATCTCTAATGCAATCGATCAGTTTGTGACCAGCACGATTGGTGAGGATGAAGA
TTTGGCCAAATGGGAAGCAATGTTTGAGGAAGTTCCTAAACTGTTAACTGATTCAGAAAAGAAGGAATGGACTGATACAC
TGAAACAAGTGTCTGTCAGTTCTGATGCATTTTTCCCTTTTAGGGATAATGTAGACAGAGCAAAAAGGAGTGGTGTAGAC
TTCATTGTGGCCCCCTCAGGTTCAACTGCTGACCACATTGTGATTGAGGCTGTGATGAGCTTGGAATTACACTCATTCAT
ACGAATCTTTGACTATTTCATCAT

Alignment

ORF - retro_mdom_1074 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.64 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GILARKSPEDQADMARLDFSLIRIVVCNLYPFVKTVASPNVTVEEAVEQIDIGGVTLLRAAAKNHARVTV
          G.LA..S.EDQ.D.ARLDFSLIRIVVCNLYPF.KTVA..NVTVEEAVEQIDIGGVTLLR.A.KN.ARVTV
Retrocopy GDLACNSAEDQPDVARLDFSLIRIVVCNLYPFMKTVAPSNVTVEEAVEQIDIGGVTLLRDATKNPARVTV

Parental  VCEPGDYEVVYTEMLNSDTKDTTMETRRQLALKAFTHTAQYDQAISDYFRKEYSKGISQIPLRYGMNPHQ
          VCEPGDYEVV.TEMLNSDTKDTTMETRRQLA.KAFT.TAQ.DQAIS.YFRKE.SKGI.QIPLRYGM.P.Q
Retrocopy VCEPGDYEVVDTEMLNSDTKDTTMETRRQLASKAFTLTAQNDQAISAYFRKESSKGIAQIPLRYGMIPRQ

Parental  KPAQLYTVKPKLPLTVLNGSPGFINLCDALNAWQLVKELREALGISAATSFK-HVSPAGAAVGVPLSEEE
          KPA.LY.VKPKLPLTVLNGSPGFINLCDALNAWQLVKELREA..ISAATSFK..VSPAGAA.GVPL.EEE
Retrocopy KPARLYPVKPKLPLTVLNGSPGFINLCDALNAWQLVKELREASSISAATSFK<GVSPAGAAIGVPLGEEE

Parental  AKVCMVHDLYKSLTPLSIAYARARGADRMSSFGDFIAVSDVCDVTTAKIISREVSDGIIAPGYEEEALKI
          ..VCMVHDLYKSLTPLS....RARGADRMSSFGDFIAVSDVCD.TTAKI.SREVSDGIIAPGYEEEALKI
Retrocopy PEVCMVHDLYKSLTPLSTGHGRARGADRMSSFGDFIAVSDVCDITTAKITSREVSDGIIAPGYEEEALKI

Parental  LSKKK-NGSYCVLQMDPCYKPEEDEIRTLFGLHLSQKRNNGVIDKSLFNNIVTKHKDLPEPAIRDLIVAT
          LSKKK.NGSYCVLQMD...KPEEDEIR.LFGLHLSQKRNNGVIDKSLFNNIVTKHKDLPEPAIRDLIVAT
Retrocopy LSKKK>NGSYCVLQMD---KPEEDEIRPLFGLHLSQKRNNGVIDKSLFNNIVTKHKDLPEPAIRDLIVAT

Parental  IAVKYTQSNSVCYAKNGQVIGIGAGQQSRIHCTRLAGDKANNWWLRHHPRVLSMKFKAGVKRAEISNAID
          IAVKYTQSNS.C.AKNGQVIG.GAGQQS.IHCTRLAGDKANNWWLRHHPRVLSMKFKAGVKRAEISNAID
Retrocopy IAVKYTQSNSACHAKNGQVIGVGAGQQS*IHCTRLAGDKANNWWLRHHPRVLSMKFKAGVKRAEISNAID

Parental  QYVTGTIGEDEDLAKWEAMFEEVPKLLTDTEKKEWIDTLKQVSVSSDAFFPFRDNVDRAKRSGVEFIVAP
          Q.VT.TIGEDEDLAKWEAMFEEVPKLLTD.EKKEW.DTLKQVSVSSDAFFPFRDNVDRAKRSGV.FIVAP
Retrocopy QFVTSTIGEDEDLAKWEAMFEEVPKLLTDSEKKEWTDTLKQVSVSSDAFFPFRDNVDRAKRSGVDFIVAP

Parental  SGSTADQIVIEA-CDELGITLIHTNLRLFHH
          SGSTAD.IVIEA.CDELGITLIHTNL.LFHH
Retrocopy SGSTADHIVIEA<CDELGITLIHTNL*LFHH

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
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1074 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1074 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011695	4 retrocopies	retro_cjac_1538, retro_cjac_2185, retro_cjac_3116, retro_cjac_706,
Microcebus murinus	ENSMICG00000014573	1 retrocopy	retro_mmur_1591,
Myotis lucifugus	ENSMLUG00000001830	1 retrocopy	retro_mluc_1370,
Monodelphis domestica	ENSMODG00000015612	1 retrocopy	retro_mdom_1074 ,
Mustela putorius furo	ENSMPUG00000007676	1 retrocopy	retro_mputfur_1609,
Mus musculus	ENSMUSG00000026192	1 retrocopy	retro_mmus_2729,
Rattus norvegicus	ENSRNOG00000015511	1 retrocopy	retro_rnor_904,