RetrogeneDB ID: retro_mdom_1913

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:109476605..109477779(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: STK38L
• Ensembl ID: ENSMODG00000016636
• Aliases: None
• Description: serine/threonine kinase 38 like [Source:HGNC Symbol;Acc:17848]

Sequence

>retro_mdom_1913
ATGGCAATGACTGCGGGGACTACAACAACTTTTCCCATTAGCAACCACACCTGGGAAAGAGTGACTGTAGCTAAACTCAC
ATTGGAGAATTTCGACAGCAACCTAATTTTACAGCATAAAGAAAGAGAAACCAGGCAAAAGAAGTTAGAGGTGGCTATGG
AAGAAGAAGGATTGGCAGATGAAGAGAAAAAATTACACCCATCACAGCATGCTCTCAAAGAAACTGAATTTCTACAATTC
AAGAGGACAAGGCTTGGTTTAGATGACTTTGAATCCCTGAAAATTATAGGGAGAGGAGCCTTTGGAGAGATACTCCTTAT
CCAGAAGAAAGATACAGGCCATATCTATGCAATGAAGATATTGAGAAGGGCTGATATGCTTGAAAAAGAACAGGTGGCCC
ATATCCGAGCAGAGAGAGATATATTGGTAGAAGCAGATGGTGCCTGGGTTGTGAAGATGTTTTATAGTTTTCAGGATAAA
AGGAATCTTTATCTCATTATGGAATTTCTCCCTGGAGGAGACATGATGACATTACTAATGAAGAAAGATACCTTGACAGA
AGAAGAAACCCAGTTCGATATTTCAGAGACTGTTCTGGCTATCGATGCAATTCACCAGTTGGGGTTCATTCACTGAGATA
TCAAACCAGACAACCTCTTATTGGATGTCAAGGGTCATGTAAAGTTGTCTGATTTTGGTCTATGCAAAGGACTAAAGAAA
GCACATAGGACTGAATTCTATAGGAACCTCACACATAACCCACCAAGTGATTTCTCATTTCAGAATATGAACTCAAAGAG
AAAAGCAGAAACATAGAAAAAAAAATAGGCGGCAATTGGCATATTCCACAGTTGGAACTCCAGATTACATTGCTCCAGAA
GTATTCATGCAGACTGGGTACAACAAATTGTGTGACTGGTGGTCTTTGGGAGTTATTATGTATGACATGCTAATAGGATA
TCCACCATTCTGTTCTGAAACACCACAAGAAACTTATAGGAAAGTTATGAACTGGAAAGAAACTCTAGTATTTCCTCCAG
AAGTACCTATATCGGAGAATGCCAAGGATCTAATTCTCAGATTTTGTATTGATTCAGAAAACAGAATTGGAAACAGTGGA
ATAGAGGAAATCAAAGATCATCCATTTTTCGAAGGAGTAGATTGGGGACACATC

Alignment

ORF - retro_mdom_1913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.15 %
• Parental protein coverage: 84.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMTAGTTTTFPMSNHTRERVTVAKLTLENFYSNLILQHEERETRQKKLEVAMEEEGLADEEKKLRRSQH
          MAMTAGTTTTFP.SNHT.ERVTVAKLTLENF.SNLILQH.ERETRQKKLEVAMEEEGLADEEKKL..SQH
Retrocopy MAMTAGTTTTFPISNHTWERVTVAKLTLENFDSNLILQHKERETRQKKLEVAMEEEGLADEEKKLHPSQH

Parental  ARKETEFLRLKRTRLGLDDFESLKVIGRGAFGEVRLVQKKDTGHIYAMKILRKADMLEKEQVAHIRAERD
          A.KETEFL..KRTRLGLDDFESLK.IGRGAFGE..L.QKKDTGHIYAMKILR.ADMLEKEQVAHIRAERD
Retrocopy ALKETEFLQFKRTRLGLDDFESLKIIGRGAFGEILLIQKKDTGHIYAMKILRRADMLEKEQVAHIRAERD

Parental  ILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFYISETVLAIDAIHQLGFI
          ILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQF.ISETVLAIDAIHQLGFI
Retrocopy ILVEADGAWVVKMFYSFQDKRNLYLIMEFLPGGDMMTLLMKKDTLTEEETQFDISETVLAIDAIHQLGFI

Parental  HRDIKPDNLLLDAKALGHVKLSDFGLCTGLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAET-WKKNRR
          H.DIKPDNLLLD.K..GHVKLSDFGLC.GLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAET.....RR
Retrocopy H*DIKPDNLLLDVK--GHVKLSDFGLCKGLKKAHRTEFYRNLTHNPPSDFSFQNMNSKRKAET>XXXXRR

Parental  QLAYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYEMLIGYPPFCSETPQETYRKVMNWKETLVFPPE
          QLAYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMY.MLIGYPPFCSETPQETYRKVMNWKETLVFPPE
Retrocopy QLAYSTVGTPDYIAPEVFMQTGYNKLCDWWSLGVIMYDMLIGYPPFCSETPQETYRKVMNWKETLVFPPE

Parental  VPISEKAKDLILRFCIDSENRIGNSGIEEIKDHPFFEGVDWGHI
          VPISE.AKDLILRFCIDSENRIGNSGIEEIKDHPFFEGVDWGHI
Retrocopy VPISENAKDLILRFCIDSENRIGNSGIEEIKDHPFFEGVDWGHI

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_1913 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1913 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
Dasypus novemcinctus	ENSDNOG00000025573	1 retrocopy	retro_dnov_1680,
Monodelphis domestica	ENSMODG00000016636	1 retrocopy	retro_mdom_1913 ,
Mus musculus	ENSMUSG00000001630	2 retrocopies	retro_mmus_3100, retro_mmus_347,