RetrogeneDB ID: retro_mdom_1416

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:370091206..370091818(-)
• Located in intron of: ENSMODG00000009913

Retrocopy information

• Ensembl ID: ENSMODG00000009970
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AAGAB
• Ensembl ID: ENSMODG00000009585
• Aliases: None
• Description: alpha- and gamma-adaptin binding protein [Source:HGNC Symbol;Acc:25662]

Sequence

>retro_mdom_1416
ATCTTGGTTTGTGACAGAGTATCTGAAAATGGTGTAAGACGACCAAGAGCTCAAGAATGGCGCATTCAACATGGCTTTGA
ATTGGTAGAACTTAATCCAGAGGAATTACCTGAGGAAGATGATGACTTTCCAGAGTCTACTGGAGTAAAGAGAATTGTAC
AAGCCTTGAATGCCAATGTATGGTCGAATGTGGTAATGAAGAGTGAAAGAAATCAAAGCTTTGGCCTTCTCAGTTCATTG
GCTGGTGCAAATTGTAACATTGGGTCAACTGAAAACCATCAAACCGAACCTTGTATGCCAGTAGGAGATAGGGCTAAAAG
CTGCTTTGATTATCAAGATAGTGCTTCTAACATAGCTGATGCCCAAGTCAATAGCATTGTGGACCCCATGTTAGACCTGG
ATATCCAAGAATTAGCCAGTCTCACTACTGGAGGAGGAGATCTGGAAAATTTGGAAAGACTATTTTCAAAACTAAAAGAA
ATGAAAGACAAAGCAGTGACTTTGCCTCATGAACAAAGAAAGTTGAATGCAGAAAAGGTGGCCAAAGCATTCTGGATGGC
AATTGGTGGAGACAGAGATGAGATTGAAGGCATTTCTTCTGATGAAGAAAAC

Alignment

ORF - retro_mdom_1416 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.1 %
• Parental protein coverage: 64.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILVCDRVSENGVSRPRAQEWCIQHGFELVELNPEELPEEDDDFPESTGVKRIVQALNANVWSNVVMKSER
          ILVCDRVSENGV.RPRAQEW.IQHGFELVELNPEELPEEDDDFPESTGVKRIVQALNANVWSNVVMKSER
Retrocopy ILVCDRVSENGVRRPRAQEWRIQHGFELVELNPEELPEEDDDFPESTGVKRIVQALNANVWSNVVMKSER

Parental  NQSFGLLSSLAGANCNIGSTENHHTEPCMPVGDRAESCFDHQDSASNTADAQVDSIVDPMLDLDIQELAS
          NQSFGLLSSLAGANCNIGSTENH.TEPCMPVGDRA.SCFD.QDSASN.ADAQV.SIVDPMLDLDIQELAS
Retrocopy NQSFGLLSSLAGANCNIGSTENHQTEPCMPVGDRAKSCFDYQDSASNIADAQVNSIVDPMLDLDIQELAS

Parental  LTTGGGDLENFERLFSKLKEMKDKAATLPHEQRKLHAEKVAKAFWMAIGGDRDEIEGISSDEEN
          LTTGGGDLEN.ERLFSKLKEMKDKA.TLPHEQRKL.AEKVAKAFWMAIGGDRDEIEGISSDEEN
Retrocopy LTTGGGDLENLERLFSKLKEMKDKAVTLPHEQRKLNAEKVAKAFWMAIGGDRDEIEGISSDEEN

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	101.91 RPM
SRP007412_cerebellum	0.00 RPM	111.32 RPM
SRP007412_heart	0.00 RPM	85.92 RPM
SRP007412_kidney	0.00 RPM	171.19 RPM
SRP007412_liver	0.00 RPM	76.03 RPM
SRP007412_testis	0.00 RPM	106.47 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1416 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1416 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000040368	1 retrocopy	retro_btau_723,
Canis familiaris	ENSCAFG00000017414	1 retrocopy	retro_cfam_1891,
Monodelphis domestica	ENSMODG00000009585	1 retrocopy	retro_mdom_1416 ,
Rattus norvegicus	ENSRNOG00000008424	2 retrocopies	retro_rnor_1443, retro_rnor_2813,