RetrogeneDB ID: retro_mdom_1999

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:49877478..49878048(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000013907
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RAB2A
• Ensembl ID: ENSMODG00000008556
• Aliases: None
• Description: RAB2A, member RAS oncogene family [Source:HGNC Symbol;Acc:9763]

Sequence

>retro_mdom_1999
GTGTTGCTACAGTTTACAGACAAGAGGTTCCAGCCTGTACATGAACTAACCATTGGTGTAGAATTTGGTGCCCGCATCAT
AACCATTGATGACAAACAGATCAAGCTCCAGATCTGGGATACAGCTGGGCAAGAATCCTTTCGATCCATCACAAGATCCT
ATTACCGTGGAGCTGCTGGAACCCTGCTGATGTATGACATTACCCAGAGACAAACATTCAATCATCTGACAACTTGGCTG
GAAGATGCCCGTCAGCATTCTAATGCCAACATGGTAGTCACACTTATTGGCAACAAAAGTGATTTGGAGACCAGACAAGA
AGTAAAGAAAGAAGAAGGAGAAGCTTTTGCCAGAGAACATGGGCTAATCTTCATGGAAACCTCAGCAAGAACTTCCACCA
ATGTAGAAGAAGCCTTTATTGATACGGCCAAGATTTATGGTAAGATCCAAGAAGGAATCTTTGATTTGAATAATGAGGCC
AATGGTATTAAGATAGGTGTTCAGCATTCCCTGGATTCTACCTTTCACGAAGGAAACCAAAGAGGATGGCATTCTAGGGG
AGGCTGTTGT

Alignment

ORF - retro_mdom_1999 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.68 %
• Parental protein coverage: 90.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLQFTDKRFQPVHDLTIGVEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRR
          .LLQFTDKRFQPVH.LTIGVEFGAR.ITID.KQIKLQIWDTAGQESFRSITRSYYRGAAG.LL.YDIT.R
Retrocopy VLLQFTDKRFQPVHELTIGVEFGARIITIDDKQIKLQIWDTAGQESFRSITRSYYRGAAGTLLMYDITQR

Parental  DTFNHLTTWLEDARQHSNSNMVIMLIGNKSDLESRREVKKEEGEAFAREHGLIFMETSAKTASNVEEAFI
          .TFNHLTTWLEDARQHSN.NMV..LIGNKSDLE.R.EVKKEEGEAFAREHGLIFMETSA.T..NVEEAFI
Retrocopy QTFNHLTTWLEDARQHSNANMVVTLIGNKSDLETRQEVKKEEGEAFAREHGLIFMETSARTSTNVEEAFI

Parental  NTAKEIYEKIQEGVFDINNEANGIKIGPQHAATNATHAGSQGGQQAGGGCC
          .TAK.IY.KIQEG.FD.NNEANGIKIG.QH......H.G.Q.G....GGCC
Retrocopy DTAK-IYGKIQEGIFDLNNEANGIKIGVQHSLDSTFHEGNQRGWHSRGGCC

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_1999 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1999 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007153	1 retrocopy	retro_cfam_2057,
Equus caballus	ENSECAG00000012124	1 retrocopy	retro_ecab_970,
Erinaceus europaeus	ENSEEUG00000007700	1 retrocopy	retro_eeur_496,
Echinops telfairi	ENSETEG00000010340	2 retrocopies	retro_etel_203, retro_etel_32,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999 , retro_mdom_989,
Monodelphis domestica	ENSMODG00000016955	1 retrocopy	retro_mdom_1710,
Mus musculus	ENSMUSG00000047187	1 retrocopy	retro_mmus_2650,
Sorex araneus	ENSSARG00000013511	2 retrocopies	retro_sara_688, retro_sara_744,
Tarsius syrichta	ENSTSYG00000013060	1 retrocopy	retro_tsyr_1215,
Tursiops truncatus	ENSTTRG00000009615	1 retrocopy	retro_ttru_1377,