RetrogeneDB ID: retro_mdom_1957

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:24410923..24412969(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000021341
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTMR10
• Ensembl ID: ENSMODG00000011784
• Aliases: None
• Description: myotubularin related protein 10 [Source:HGNC Symbol;Acc:25999]

Sequence

>retro_mdom_1957
TTTCAGAAATTTCATTATACAAACCTTCTCCTTGGTGAACATGATGTACCTTTAACATGTATTGAGCAAATTGTAACAGT
AAATGACAACAAAAGGAAACAGAAGATACTAGGCCCCAACCAGAAACTCAAATTTAATCCTACAGAGCTAATTATCTATT
GTAAAGATTTCAGAATTGTCAGATTTCGCTTTGATGAAGCAGGTCCTGAAAGTGCCAAAAAGGTGTGCCTTGCGATAGCT
CATTATTCTCAGCCAACTGATCTCCAGCTACTCTTTGCATTTGAATACGTTGGGGAAAAGTACCACAATACAGCTAAAAA
TATTAATGGAATAGACTCTGGAAGTGGAGGAATACCTGGTGGTAATAGTCAAAAAACTCCTTTATTTGAAACTTTCTCTG
ATTGGGATAGAGAAATCAAAAGGACAGGTGCCTCAGAATGGAGAGTTTGTTCAATTAATGAGGGCTACATGATTTCTACT
TGCCTTCCAGAATATTTTGTAGTTCCATCTTCTTTGGCAGATCAAGATCTAAAACTCTATTCTCATTCTGTTTTTGGGAG
GCGGATGCCATTATGGTGCTGGAATCACTCTAATGGCAGTGCTCTTATAAGAATGGCCCTCATAAAAGATGTATTGCAAC
AGAAAAAAATAGATCAAAGGATTTGTACTGCAATAACCAAAAGTCATCCACAGAGGAGTGATGTGTACAAATCTGATTTG
GATAAGAATTTGCCTAGTATTCAAGAAATACAAGCTGCATTTGTAAAACTTAAGCAACTCTGTGTTGATGAGCCTTATGA
GGAAACAGAAGTGAAATGGTTGTCTTCACTGGAAAATACTCGCTGGTTAGAGTATGTTAGAGCATTCCTAAAGTATTCTG
CTGAGCTTGTATATGTGCTGGAAAGTAAACATCTTTCAGTTATCCTTAGAGAGGAAGAAGGAAGGGATCTGAGTTGTTTC
GTAGCTTCTCTCATTCAAGTGATGCTGGATCCTCATTTTCGAACAATTACTGGATTTCAAAGTTTGATACAGAAAGAATG
GGTCATGGCAGGATATCGATTTCTAGACAGATGTAACCACTTAAATAGATCTGCAAAAGAGTCTCCCTTATTCTTGTTAT
TTCTGGACTCCATCTGGCAGCTGTTAGAGCAATATCCAGCAGCCTTTGAATTTTCAGAAACTTATTTAATGTTGCTGTAT
GACAGTACACGGATCTCATTGTTTGGCACTTTTCTTTTCAACTCTCCTCATCAGCGAGTAAAACAAAGCACAGAATTTGC
TATTAGCAAAAATATACAACTCGGTGATGAAAAGGGCTTAAAATTTCCGTCGGTTTGGGACTGGTCTCTTCAATTTGCAG
CAAAGGATCGCACCCTTTTTAATAATCCCTTATACATTGGAAAGAGTGCACCATGTGTACAAAATGGGTCAGTGAAATCA
TTTAAGCGGACAAAGAAAAATTATAGCTCTACATTAAGAGGAATGCCACCTTCCTTTAAGAATGGACTCATCAATGATCA
AGATTTGCTTCCAAGGAGAAATTCACTAATATTGAAATTAAAGACTGATATAGAGCAAACTGACAGCCAGAGCACTGATA
TGGAGCAATATTTTAGAGACTGGTTTTCAAAACCTGTTGACCTGCATGGTGTAATTCTACCCCGCATTTCGGGAATACAC
ATAAAACTGTGGAAACTCTGCTACTTCCGTTGGGTTCCAGAGGCTCAGATTAATAATGGTGGCTTCATTATAGCATTTCA
TAGAATATCTCTTCTGACAGATGAAATAGATATGCTCAGCAGGAGTCTTCGACAGTACAAGAGCAATTCCTCGCAATCCA
GCTATTCAGAACTGGATCAGAGTAGGATGTACTTTAAAGCAAATGGTATAAATGATACATCTGGGACGCCAGAGTTTCTT
TCCTCTTCATTTCCGTTTTCACCTATAGGGAACCTTTGCAGAAGAAGCATTTTAGGAACACCATTAAGCAAATTTTTAAA
TGGTGCCAAAATATGGCTGTCTACTGAGACACTAGCAAATGAGGAC

Alignment

ORF - retro_mdom_1957 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FQKFHYTNLLLGEHDVPLTCIEQIVTVNDNKRKQKILGPNQKLKFNPTELIIYCKDFRIVRFRFDEAGPE
          FQKFHYTNLLLGEHDVPLTCIEQIVTVNDNKRKQKILGPNQKLKFNPTELIIYCKDFRIVRFRFDEAGPE
Retrocopy FQKFHYTNLLLGEHDVPLTCIEQIVTVNDNKRKQKILGPNQKLKFNPTELIIYCKDFRIVRFRFDEAGPE

Parental  SAKKVCLAIAHYSQPTDLQLLFAFEYVGEKYHNTAKNINGIDSGSGGIPGGNSQKTPLFETFSDWDREIK
          SAKKVCLAIAHYSQPTDLQLLFAFEYVGEKYHNTAKNINGIDSGSGGIPGGNSQKTPLFETFSDWDREIK
Retrocopy SAKKVCLAIAHYSQPTDLQLLFAFEYVGEKYHNTAKNINGIDSGSGGIPGGNSQKTPLFETFSDWDREIK

Parental  RTGASEWRVCSINEGYMISTCLPEYFVVPSSLADQDLKLYSHSFFGRRMPLWCWNHSNGSALIRMALIKD
          RTGASEWRVCSINEGYMISTCLPEYFVVPSSLADQDLKLYSHS.FGRRMPLWCWNHSNGSALIRMALIKD
Retrocopy RTGASEWRVCSINEGYMISTCLPEYFVVPSSLADQDLKLYSHSVFGRRMPLWCWNHSNGSALIRMALIKD

Parental  VLQQKKIDQRICTAITKSHPQRSDVYKSDLDKNLPSIQEIQAAFVKLKQLCVDEPYEETEVKWLSSLENT
          VLQQKKIDQRICTAITKSHPQRSDVYKSDLDKNLPSIQEIQAAFVKLKQLCVDEPYEETEVKWLSSLENT
Retrocopy VLQQKKIDQRICTAITKSHPQRSDVYKSDLDKNLPSIQEIQAAFVKLKQLCVDEPYEETEVKWLSSLENT

Parental  RWLEYVRAFLKYSAELVYVLESKHLSVILREEEGRDLSCFVASLIQVMLDPHFRTITGFQSLIQKEWVMA
          RWLEYVRAFLKYSAELVYVLESKHLSVILREEEGRDLSCFVASLIQVMLDPHFRTITGFQSLIQKEWVMA
Retrocopy RWLEYVRAFLKYSAELVYVLESKHLSVILREEEGRDLSCFVASLIQVMLDPHFRTITGFQSLIQKEWVMA

Parental  GYRFLDRCNHLNRSAKESPLFLLFLDSIWQLLEQYPAAFEFSETYLMLLYDSTRISLFGTFLFNSPHQRV
          GYRFLDRCNHLNRSAKESPLFLLFLDSIWQLLEQYPAAFEFSETYLMLLYDSTRISLFGTFLFNSPHQRV
Retrocopy GYRFLDRCNHLNRSAKESPLFLLFLDSIWQLLEQYPAAFEFSETYLMLLYDSTRISLFGTFLFNSPHQRV

Parental  KQSTEFAISKNIQLGDEKGLKFPSVWDWSLQFAAKDRTLFNNPLYIGKSAPCVQNGSVKSFKRTKKNYSS
          KQSTEFAISKNIQLGDEKGLKFPSVWDWSLQFAAKDRTLFNNPLYIGKSAPCVQNGSVKSFKRTKKNYSS
Retrocopy KQSTEFAISKNIQLGDEKGLKFPSVWDWSLQFAAKDRTLFNNPLYIGKSAPCVQNGSVKSFKRTKKNYSS

Parental  TLRGMPPSFKNGLINDQDLLPRRNSLILKLKTDIEQTDSQSTDMEQYFRDWFSKPVDLHGVILPRISGIH
          TLRGMPPSFKNGLINDQDLLPRRNSLILKLKTDIEQTDSQSTDMEQYFRDWFSKPVDLHGVILPRISGIH
Retrocopy TLRGMPPSFKNGLINDQDLLPRRNSLILKLKTDIEQTDSQSTDMEQYFRDWFSKPVDLHGVILPRISGIH

Parental  IKLWKLCYFRWVPEAQINNGGFITAFHRISLLTDEIDMLSRSLRQYKSNSSQSSYSELDQSRMYFKANGI
          IKLWKLCYFRWVPEAQINNGGFI.AFHRISLLTDEIDMLSRSLRQYKSNSSQSSYSELDQSRMYFKANGI
Retrocopy IKLWKLCYFRWVPEAQINNGGFIIAFHRISLLTDEIDMLSRSLRQYKSNSSQSSYSELDQSRMYFKANGI

Parental  NDTSGTPEFLSSSFPFSPIGNLCRRSILGTPLSKFLNGAKIWLSTETLANED
          NDTSGTPEFLSSSFPFSPIGNLCRRSILGTPLSKFLNGAKIWLSTETLANED
Retrocopy NDTSGTPEFLSSSFPFSPIGNLCRRSILGTPLSKFLNGAKIWLSTETLANED

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	8.22 RPM
SRP007412_cerebellum	0.00 RPM	6.86 RPM
SRP007412_heart	0.00 RPM	5.38 RPM
SRP007412_kidney	0.00 RPM	27.65 RPM
SRP007412_liver	0.00 RPM	17.12 RPM
SRP007412_testis	0.00 RPM	7.07 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1957 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1957 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012336	1 retrocopy	retro_chof_1162,
Monodelphis domestica	ENSMODG00000011784	2 retrocopies	retro_mdom_1377, retro_mdom_1957 ,
Ictidomys tridecemlineatus	ENSSTOG00000008851	1 retrocopy	retro_itri_1894,