RetrogeneDB ID: retro_mdom_1885

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:232240001..232240755(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006396
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IRAK1BP1
• Ensembl ID: ENSMODG00000018444
• Aliases: None
• Description: interleukin-1 receptor-associated kinase 1 binding protein 1 [Source:HGNC Symbol;Acc:17368]

Sequence

>retro_mdom_1885
GATAGGATTCAGGATGGCTTCTCGGGCGCCGCTGGTGAGACCCTGCTGAACCTCAACAGCCATTTGTCCCTATGCGTGCC
CCGGCTTCAGCCCTGTCCTCAACTCCACCCCTGGCCCCAAATCCGCCCTGTGAGGTGCACGTGAGGGGCTCAGCAGAAAT
GTCCTGTGTTCCCAACTGGGCCCTGGTTACGGTGAAGGTCAGCAGCACCAAAAACTCGGCCTCTGAGGCCAAGAACAGAG
TGAGCCGCTGCCTGGACTACATCACACAGAACCTGCAGAAACCAGACGTGCAGGCAGAAAATATAACTGTGACAAAGGAT
ATTAGTAGAATAGGAAATGCTTATCACATGGAAGCAGAGGTCAGCATTATATTCTCCGAATTCGAAAAAATGCAGGATAT
TTGTAATCTTTTCGTGGAAAAACTAGATAGTTCTGTTATTATCAATCCTCCTCACTTTAACATACACCAGGAGTTATTGA
GAATCTTAGACGTCAAGTTTGTCTCTGTGCTGTTGGAAATGCATGGCGAAAAGCTCAAGAAGTATGTCAGCTTGTTGGTC
AGTCACTAGGAAAATCTTTATTAATCAAAGAAGAGGAAATAAAAGAATGGGAAGGGCAGATAGACAATCAGCAATTATCT
GACCTTGCAAGTTCTCTAAGTATGCAACAGAAAATCCAAACTGCAACTATATATGTTTCTTCCAGGGTATTTTTAAACTT
CGAGGTTAAGAAAAAGGAAAAGAAGAAAAAGATT

Alignment

ORF - retro_mdom_1885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.7 %
• Parental protein coverage: 70.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DRIQDGFSGAAGETLPNLNSHLPLCA-APASALSSAPPPAPNPPREVHVRGSAELSCVPDRALVTVKVSS
          DRIQDGFSGAAGETL.NLNSHL.LC..APASALSS.PP.APNPP.EVHVRGSAE.SCVP..ALVTVKVSS
Retrocopy DRIQDGFSGAAGETLLNLNSHLSLCV<APASALSSTPPLAPNPPCEVHVRGSAEMSCVPNWALVTVKVSS

Parental  TKNSASEAKNSVSRRLDYITQNLQKPDVQAENITVTKDISRIGNAYHMEAEVSIIFSEFEKMQDICNLFV
          TKNSASEAKN.VSR.LDYITQNLQKPDVQAENITVTKDISRIGNAYHMEAEVSIIFSEFEKMQDICNLFV
Retrocopy TKNSASEAKNRVSRCLDYITQNLQKPDVQAENITVTKDISRIGNAYHMEAEVSIIFSEFEKMQDICNLFV

Parental  EKLDSSVIINPPHFY-HTPGAIENLRRQVCLCAVGNAWRKAQEVCQLVGQSLGKPLLIKEEEIKEWEGQI
          EKLDSSVIINPPHF..HTPG.IENLRRQVCLCAVGNAWRKAQEVCQLVGQSLGK.LLIKEEEIKEWEGQI
Retrocopy EKLDSSVIINPPHFN<HTPGVIENLRRQVCLCAVGNAWRKAQEVCQLVGQSLGKSLLIKEEEIKEWEGQI

Parental  DNQQLSDLASSLSMQQKIQTATIYVSSRVFLNFEVKKKEKKKKI
          DNQQLSDLASSLSMQQKIQTATIYVSSRVFLNFEVKKKEKKKKI
Retrocopy DNQQLSDLASSLSMQQKIQTATIYVSSRVFLNFEVKKKEKKKKI

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_1885 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1885 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012945	1 retrocopy	retro_amel_783,
Canis familiaris	ENSCAFG00000002793	1 retrocopy	retro_cfam_429,
Monodelphis domestica	ENSMODG00000018444	1 retrocopy	retro_mdom_1885 ,
Oryctolagus cuniculus	ENSOCUG00000001488	1 retrocopy	retro_ocun_347,