RetrogeneDB ID: retro_mdom_859

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:226844279..226846463(-)
• Located in intron of: ENSMODG00000023922

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNMT3A
• Ensembl ID: ENSMODG00000015850
• Aliases: None
• Description: DNA (cytosine-5-)-methyltransferase 3 alpha [Source:HGNC Symbol;Acc:2978]

Sequence

>retro_mdom_859
AGGAGGACACAGTCTGAGCTTCTGGGCCAAGGGGGCTCACACCTGAGCTGGACCAGACAGAGGTTGCACCTGGCCTTATG
GGCTGAGAAGAAAGCCAAGGTCATTGCAGTGATGAATGTCGTAGAAGAAAACCAGGGGCCTGGGGAGCCACAAAAAGTGG
AGGAGGCCAGTCCTCCTATTTTGCAACAACCTACTGATGATGCTTCTCCCACTGTGGCCACCACACCTGAGCCAGTGGGG
GCTGATGCTGGGGACAAGAATACTGCCAAGGCTGCTGCTGATGAGCCTGAATATGAGGATGGCCGAGACTTTGGTATTGG
GGAGTTGGTATGGGGAAAACTTCGAGGCTTCTCCTGGTGGCCTGGCCGAATTGTATCCTGGTGGATGACAGGCAGAAGCC
GAGCAGCTGAAGGCACTCGATGGGTCATGTGGTTTGGAGATGGCAAGTTCTCAGTGGTTTGTGTTGAGAAATTGATGCCA
CTGAGCTCCTTCTGCAGCGCCTTCCACCAAGCCACATATAACAAGCAGCCTATGTACCGGAAAGCCATCTATGAGGTCCT
TCAGGTGGCCAGCAGCCGCACTGGGAAGCTGTTTCCGGCCTGCCCGGAGAATGATGAAAGTGACACAGCCAAGGCAGTGG
AGTTGCAGAACAAGCAAATGATCGAATGGGCTCTGGGTGGCTTCCAGCCCTCTGGCCCCAAGGGCCTGGAGCCACCAGAA
GAAGAGAGAAATCCCTACAAAGAAGTTTACACTGATATGTGGGCCCCAGTAGAGCCTGAAGCTGCTGCCTATGCCCCACC
TCCACCAGCCAAAAAACCCCGAAAGAGCACAGCAGAGAAGCCCAAGATCAAAGAGATCATTGATGAACGCACAAGAGAGC
GGCTGGTATATGAGGTGCGGCAGAAGTGCAGGAATATCGAAGACATCTGCATCTCCTGTGGGAATCTCAACGTCACCCTG
GAACACCCCCTCTTCATCGGAGGAATGTGCCAAAACTGCAAGAACTGATTCCTGGAGTGTGCCTATCAGTACGACGATGA
CGGCTACCAGTCATATTGTACTATCTGCTGTGGGGGTCGAGAGGTCCTCATGTGTGGGAACAACAACTGTTGCAGGTGCT
TCTGTGTGGAATGTGTGGACCTGTTGGTGGGACCAGGTGCTGCCCAGGCAGCCATCAAGGAAGACCCCTGGAACTGCTAC
ATGTGTGGGCACAAAGGCACCTATGGGCTGCTGCGGCGGCGAGATGACTGGCCGTCGTGCCTCCAGATGTTTTTCGCCAA
TAACCATGACTAAGAGTTTGACCCTCCCAAAGTTTATCCCCCAGTCCCAGCTGAAAAACGGAAGCCAATCCGGGTGCTAT
CTCTTTTCGATGGAATTGCCACAGAACTATTGGTGCTGAAGGACCTGGGGATCCAGGTAGACCGCTACATTGCCTCAGAG
GTGTGTGAGGACTCCATCACTGTGGGCATGGTGCGGCACCAAGGGAAGATCATGTACGTGGGGGACGTCCGCAATGTCAC
CCAGAAGCACATACAGGAATGGGGCCCTTTTGATTTGGTGATTGGAGGCAGTCCCTGCAATGATCTTTCTATTGTCAACC
CTGCTCGGAAGGGTCTTTATGAGGGCACTGGACGGTTCTTCTTTGAGTTCTACCACCTTCTGCATGAGGCCCGGCCCAAG
GAGGGCGATGATCGCCCCTTCTTCTGGCTCTTTGAAAACGTGGTGGCCATGGGGGTCAGTGATAAGCGGGACATCTCACG
CTTTCTAGAGTCCAACCCTGTGATGATTGATGCCAAAGAAGTGTCAGCAGCGCACAGGGCTCGCTACTTTTGGGGTAACC
TTCCCGGTATGAACAGGCCATTGGCATCTACCGTGAATGATAAGCTGGAGCTTCAGGAATGTTTGGAGCATGGCAGGATA
GCCAAGTTCAGCAAAGTGAGGACCATTACGACTAGGTCAAACTCCATCAAGCAGGGCAAAGACCAGCATTTCCCTGTCTT
CTTGAATGAGAAAGAGGACATCTTGTGGTGCACTGAAATGGAAAGGGTCTTTGGCTTCCCAGTCCATTACACGGATGTCT
CCAACATGAGCCGTTTGGCAAGGCAAAGACTGCTGGGCCGGTCATGGAGTGTGCCTGTGATTCGCCACCTCTTTGCCCCC
TTGAAGGAATATTTTGCCTGTGTG

Alignment

ORF - retro_mdom_859 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.68 %
• Parental protein coverage: 85.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRPMQRLTFQAGDPYYISKRKRDEWLARWKREAEKKAKVIAVMNVVEENQGPGEPQKVEEASPPTLQQPT
          .R....L..Q.G.....S.......LA.W...AEKKAKVIAVMNVVEENQGPGEPQKVEEASPP.LQQPT
Retrocopy RRTQSELLGQGGS--HLSWTRQRLHLALW---AEKKAKVIAVMNVVEENQGPGEPQKVEEASPPILQQPT

Parental  DPASPTVATTPEPVGADAGDKNTAKASDDEPEYEDGRGFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRA
          D.ASPTVATTPEPVGADAGDKNTAKA..DEPEYEDGR.FGIGELVWGKLRGFSWWPGRIVSWWMTGRSRA
Retrocopy DDASPTVATTPEPVGADAGDKNTAKAAADEPEYEDGRDFGIGELVWGKLRGFSWWPGRIVSWWMTGRSRA

Parental  AEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSAFHQATYNKQPMYRKAIYEVLQVASSRAGKLFPACPEND
          AEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSAFHQATYNKQPMYRKAIYEVLQVASSR.GKLFPACPEND
Retrocopy AEGTRWVMWFGDGKFSVVCVEKLMPLSSFCSAFHQATYNKQPMYRKAIYEVLQVASSRTGKLFPACPEND

Parental  ESDTAKAVEVQNKQMIEWALGGFQPSGPKGLEPPEEERNPYKEVYTDMWAPVEPEAAAYAPPPPAKKPRK
          ESDTAKAVE.QNKQMIEWALGGFQPSGPKGLEPPEEERNPYKEVYTDMWAPVEPEAAAYAPPPPAKKPRK
Retrocopy ESDTAKAVELQNKQMIEWALGGFQPSGPKGLEPPEEERNPYKEVYTDMWAPVEPEAAAYAPPPPAKKPRK

Parental  STAEKPKIKEIIDERTRERLVYEVRQKCRNIEDICISCGSLNVTLEHPLFIGGMCQNCKNCFLECAYQYD
          STAEKPKIKEIIDERTRERLVYEVRQKCRNIEDICISCG.LNVTLEHPLFIGGMCQNCKN.FLECAYQYD
Retrocopy STAEKPKIKEIIDERTRERLVYEVRQKCRNIEDICISCGNLNVTLEHPLFIGGMCQNCKN*FLECAYQYD

Parental  DDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRRD
          DDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRRD
Retrocopy DDGYQSYCTICCGGREVLMCGNNNCCRCFCVECVDLLVGPGAAQAAIKEDPWNCYMCGHKGTYGLLRRRD

Parental  DWPSRLQMFFANNHDQEFDPPKVYPPVPAEKRKPIRVLSLFDGIATGLLVLKDLGIQVDRYIASEVCEDS
          DWPS.LQMFFANNHD.EFDPPKVYPPVPAEKRKPIRVLSLFDGIAT.LLVLKDLGIQVDRYIASEVCEDS
Retrocopy DWPSCLQMFFANNHD*EFDPPKVYPPVPAEKRKPIRVLSLFDGIATELLVLKDLGIQVDRYIASEVCEDS

Parental  ITVGMVRHQGKIMYVGDVRNVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRLFFEFYRLLH
          ITVGMVRHQGKIMYVGDVRNVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGR.FFEFY.LLH
Retrocopy ITVGMVRHQGKIMYVGDVRNVTQKHIQEWGPFDLVIGGSPCNDLSIVNPARKGLYEGTGRFFFEFYHLLH

Parental  EARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTV
          EARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTV
Retrocopy EARPKEGDDRPFFWLFENVVAMGVSDKRDISRFLESNPVMIDAKEVSAAHRARYFWGNLPGMNRPLASTV

Parental  NDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVFMNEKEDILWCTEMERVFGFPVHYTDVSN
          NDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVF.NEKEDILWCTEMERVFGFPVHYTDVSN
Retrocopy NDKLELQECLEHGRIAKFSKVRTITTRSNSIKQGKDQHFPVFLNEKEDILWCTEMERVFGFPVHYTDVSN

Parental  MSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV
          MSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV
Retrocopy MSRLARQRLLGRSWSVPVIRHLFAPLKEYFACV

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	69.61 RPM
SRP007412_cerebellum	0.00 RPM	145.93 RPM
SRP007412_heart	0.00 RPM	48.24 RPM
SRP007412_kidney	0.00 RPM	68.48 RPM
SRP007412_liver	0.00 RPM	50.85 RPM
SRP007412_testis	0.00 RPM	40.27 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_859 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_859 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008172	2 retrocopies	retro_cjac_4163, retro_cjac_899,
Microcebus murinus	ENSMICG00000004108	2 retrocopies	retro_mmur_1086, retro_mmur_797,
Monodelphis domestica	ENSMODG00000015850	1 retrocopy	retro_mdom_859 ,
Oryctolagus cuniculus	ENSOCUG00000024688	1 retrocopy	retro_ocun_564,