RetrogeneDB ID: retro_mdom_1781

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:77721844..77723284(-)
• Located in intron of: ENSMODG00000003945

Retrocopy information

• Ensembl ID: ENSMODG00000003955
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNMT
• Ensembl ID: ENSMODG00000021415
• Aliases: None
• Description: RNA (guanine-7-) methyltransferase [Source:HGNC Symbol;Acc:10075]

Sequence

>retro_mdom_1781
ATGGAAAATTCTGCAAAAACAGAAGATTGTGAAAAGATCTTTGAAGATGAAGAGGCAGATGTAGTTTACAAAACAGAACT
CTCTGTCACTGTTAATGAAAATTTAACAATTTCAAAAAGTGAATCTTCTGATGGAAAGGACACTAATAGTGTACAGGAGG
TCACACCAAGAAAAAGAAAACTGGAATTTCAGGATGATCCTGATGTTGAGACTGCAAGTTGTGGGGAAGGCACTCCATCA
AAAACAAGAAAGGTAGATAATGAAATTATTCTTGAGGAAAGAGCTGCAGCAGGGGATGAAGAGGGCATTTCACGAAAGAG
AAAGTTAGAAACTGATGATGTTTCAAAAGATGATACTTCTACTTGTGGAGGTGGCACTCCTTCAAGAAAGAGAAAATTGG
AAGGTGAAGATATTCCTGTGAAACGCAAACCCTTAGAAGGACATGGCGCAACAGTAGCTGCTTACTACAATGAGCTTCAG
GAAGTTGGCTTGGAGAAACGAAGCCAGAGTCGAATTTTTTATCTTCGAAATTTTAATAATTGGATAAAGAGTGTCCTCAT
TGGGGAATTTTTAGAAAAAGTGCGACAGAAAAAGAAACGTCACATCACTGTATTGGATCTGGGATGCGGGAAAGGTGGAG
ATTTACTCAAGTGGAAAAAGGGCAAAATTAGCAAATTAGTTTGTACTGATATTGCTGATGTTTCCATCCAGCAGTGTCAG
CAGCGTTATACTGAAATGAAGAATCACTGCCGTGATCATGAGTATATTTTCAGTGCAGAATTTGTAACTGCTGACAGCTC
AAAGGAACTTTTGACTGATAAATTTCGTGATCCAGAGATTTGCTTTGATATTTGCAGTTGTCAATTTGTATTTCATTACT
CATTTGAGACTTATGAACAGGCTGATATGATGCTCAGAAATGCTTGTGGGAAACTTAGTCCTGGAGGATATTTTATTGGT
ACTACCCCAAATAGCTTTGAGCTCATAAAACGCCTTGAAGCTTCAGAAACAGAATCATTTGGAAATGAAATCTATACCAT
AAGATTTCAGAAGAAGGGAGAATATCCTTTATTTGGATGCAAATATGATTTTAACTTGGAGGGTGTTGTGGATGTTCCAG
AATTTTTGGTTTATTTTCCTTTGCTGATTGAAATGGCAAAGAAGTATAAGATGAAGTTAGTGTACAAAAAGACATTTTTG
GAATTCTATGAAGAAAAGATTAAGAACATTGAAAATAAAATGCTTCTAAAACGTATGCAGGGATTAGAGCCGTATCCAGC
AAATGAGAATGCCAAACTTGCCTCGGGGAATGTGGGTGATTATGAACATGCTGCAAAATATATGAAAAATAGTCAAGTTA
GATTACCTTTGGGAACCTTAAGTAAATCTGAATGGGAAGCTACAAGTATTTACTTGGTTTTTGCATTTGAAAAGCAACCT

Alignment

ORF - retro_mdom_1781 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MENSAKTEDCEKIFEDEEADVVSKTELSVNVNENLTISRSESSDGKDTNSVQEVTPRKRKLEFQDDPDVE
          MENSAKTEDCEKIFEDEEADVV.KTELSV.VNENLTIS.SESSDGKDTNSVQEVTPRKRKLEFQDDPDVE
Retrocopy MENSAKTEDCEKIFEDEEADVVYKTELSVTVNENLTISKSESSDGKDTNSVQEVTPRKRKLEFQDDPDVE

Parental  TASCGEGTPSKTRKVDNEIILEERAAAGDEEGISRKRKLETDDVSKDDTSTCGGGTPSRKRKLEGEDVPL
          TASCGEGTPSKTRKVDNEIILEERAAAGDEEGISRKRKLETDDVSKDDTSTCGGGTPSRKRKLEGED.P.
Retrocopy TASCGEGTPSKTRKVDNEIILEERAAAGDEEGISRKRKLETDDVSKDDTSTCGGGTPSRKRKLEGEDIPV

Parental  KRKRLEGHGSTVAAYYNELQEVGLEKRSQSRIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCG
          KRK.LEGHG.TVAAYYNELQEVGLEKRSQSRIFYLRNFNNW.KSVLIGEFLEKVRQKKKR.ITVLDLGCG
Retrocopy KRKPLEGHGATVAAYYNELQEVGLEKRSQSRIFYLRNFNNWIKSVLIGEFLEKVRQKKKRHITVLDLGCG

Parental  KGGDLLKWKKGKISKLVCTDIADVSIQQCQQRYTDMKNHCRDHEYIFSAEFVTADSSKELLTDKFRDPEM
          KGGDLLKWKKGKISKLVCTDIADVSIQQCQQRYT.MKNHCRDHEYIFSAEFVTADSSKELLTDKFRDPE.
Retrocopy KGGDLLKWKKGKISKLVCTDIADVSIQQCQQRYTEMKNHCRDHEYIFSAEFVTADSSKELLTDKFRDPEI

Parental  CFDICSCQFVYHYSFETYEQADMMLRNACGKLSPGGYFIGTTPNSFELIKRLEASETESFGNEIYTIRFQ
          CFDICSCQFV.HYSFETYEQADMMLRNACGKLSPGGYFIGTTPNSFELIKRLEASETESFGNEIYTIRFQ
Retrocopy CFDICSCQFVFHYSFETYEQADMMLRNACGKLSPGGYFIGTTPNSFELIKRLEASETESFGNEIYTIRFQ

Parental  KKGEYPLFGCKYDFNLEGVVDVPEFLVYFPLLIEMAKKYNMKLVYKKTFLEFYEEKIKNIENKMLLKRMQ
          KKGEYPLFGCKYDFNLEGVVDVPEFLVYFPLLIEMAKKY.MKLVYKKTFLEFYEEKIKNIENKMLLKRMQ
Retrocopy KKGEYPLFGCKYDFNLEGVVDVPEFLVYFPLLIEMAKKYKMKLVYKKTFLEFYEEKIKNIENKMLLKRMQ

Parental  ALEPYPANENAKLASGNVGDYEHAAKYMKNSQVRLPLGTLSKSEWEATSIYLVFAFEKQP
          .LEPYPANENAKLASGNVGDYEHAAKYMKNSQVRLPLGTLSKSEWEATSIYLVFAFEKQP
Retrocopy GLEPYPANENAKLASGNVGDYEHAAKYMKNSQVRLPLGTLSKSEWEATSIYLVFAFEKQP

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_1781 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1781 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000000172	1 retrocopy	retro_cfam_1929,
Cavia porcellus	ENSCPOG00000011388	1 retrocopy	retro_cpor_442,
Monodelphis domestica	ENSMODG00000021415	1 retrocopy	retro_mdom_1781 ,
Tupaia belangeri	ENSTBEG00000005594	1 retrocopy	retro_tbel_4062,