RetrogeneDB ID: retro_mdom_436

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:523072411..523073251(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYP51A1
• Ensembl ID: ENSMODG00000010610
• Aliases: None
• Description: cytochrome P450, family 51, subfamily A, polypeptide 1 [Source:HGNC Symbol;Acc:2649]

Sequence

>retro_mdom_436
GAAAATGCATATGAGAAGTATGGACCTGTATTTAGTTTTACAATGGTGGGCAAGAAGTTTACATACCTCCTTGGCAGTGA
AGCTGCTGCCCTGCTCTTCAACAGCAAGAATGAAGATTTGAATGCAGAAGATGTTTATGGCCGGCTCACTACCCCAGTCT
TTGGAAAGGGAGTTGCTTATGATGTGCCCAATCCAGTATTCTTGGAACAAAAGAAAATGTTAAAAACTGGCCTTAATATA
GCCCAATTTAAACAACATGTTTCCATAATTGAAAAAGAAACAAAGGAATACTTTGAAAGCTGGGGAGAAAGTGGAGAAAA
AAACTTATTTGAAGCCCTTTCTGAGCTAATCATTCTCACGGCTAGCCACTGTTTACATGGAAAAGAAATCAGAAACCAGC
TGAATGAAAAAGTGGCCCAGCTCTATGCAGATCTAGATGGAGGCTTCACCCATGCTGCTTGGCTCCTACCAGGTTGTCTG
CCTTTGCCCAGTTTCAGGCGCCGGGACCAAGTACATCAAGCAATCAAAAGCATTTTCCATAATGCAATCCAGAAACGTAG
GGAGTCAAAAGAAAAATATGATAATTTCCTCCAAACTTTGCTAGATTCTACCTACAAGGATGGGCATTCTTTGACAGATG
ATGAAATTGCAGGGCTGCTTATTGGACTTCTGTTAGCAGGGCAGCACACGTCATCCACCACAAGTGCTTGGATGGGCTTC
TTTTTGGCCAGAGACAAAATACTTCAGGAAAAATGTTACTTAGAATAGCGGAATGTCTGTGGAGAAGATTTGCCTCCTTT
ACACTATGATCAGCTCAAAGATCTACAGCTGCTTAAAAAG

Alignment

ORF - retro_mdom_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.36 %
• Parental protein coverage: 56.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENAYEKYGPVFSFTMVGKKFTYLLGSEAAALLFNSKNEDLNAEDVYGRLTTPVFGKGVAYDVPNPVFLEQ
          ENAYEKYGPVFSFTMVGKKFTYLLGSEAAALLFNSKNEDLNAEDVYGRLTTPVFGKGVAYDVPNPVFLEQ
Retrocopy ENAYEKYGPVFSFTMVGKKFTYLLGSEAAALLFNSKNEDLNAEDVYGRLTTPVFGKGVAYDVPNPVFLEQ

Parental  KKMLKTGLNIAQFKQHVSIIEKETKEYFESWGESGEKNLFEALSELIILTASHCLHGKEIRSQLNEKVAQ
          KKMLKTGLNIAQFKQHVSIIEKETKEYFESWGESGEKNLFEALSELIILTASHCLHGKEIR.QLNEKVAQ
Retrocopy KKMLKTGLNIAQFKQHVSIIEKETKEYFESWGESGEKNLFEALSELIILTASHCLHGKEIRNQLNEKVAQ

Parental  LYADLDGGFTHAAWLLPGWLPLPSFRRRDRAHQAIKSIFHNAIQKRRESKEKYDDFLQTLLDSTYKDGRS
          LYADLDGGFTHAAWLLPG.LPLPSFRRRD..HQAIKSIFHNAIQKRRESKEKYD.FLQTLLDSTYKDG.S
Retrocopy LYADLDGGFTHAAWLLPGCLPLPSFRRRDQVHQAIKSIFHNAIQKRRESKEKYDNFLQTLLDSTYKDGHS

Parental  LTDDEIAGLLIGLLLAGQHTSSTTSAWMGFFLARDKTLQEKCYLEQRSVCGEDLPPLHYDQLKDLHMLDR
          LTDDEIAGLLIGLLLAGQHTSSTTSAWMGFFLARDK.LQEKCYLE.R.VCGEDLPPLHYDQLKDL..L..
Retrocopy LTDDEIAGLLIGLLLAGQHTSSTTSAWMGFFLARDKILQEKCYLE*RNVCGEDLPPLHYDQLKDLQLLKK

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	1.07 RPM	0.00 RPM
SRP007412_cerebellum	1.31 RPM	0.00 RPM
SRP007412_heart	0.20 RPM	0.00 RPM
SRP007412_kidney	2.63 RPM	0.00 RPM
SRP007412_liver	1.51 RPM	0.00 RPM
SRP007412_testis	0.98 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_436 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_436 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005722	1 retrocopy	retro_amel_1512,
Homo sapiens	ENSG00000001630	2 retrocopies	retro_hsap_1248, retro_hsap_2807,
Gorilla gorilla	ENSGGOG00000011496	1 retrocopy	retro_ggor_1952,
Loxodonta africana	ENSLAFG00000000066	1 retrocopy	retro_lafr_272,
Monodelphis domestica	ENSMODG00000010610	1 retrocopy	retro_mdom_436 ,
Pongo abelii	ENSPPYG00000017824	2 retrocopies	retro_pabe_1039, retro_pabe_1040,
Pan troglodytes	ENSPTRG00000019391	2 retrocopies	retro_ptro_1901, retro_ptro_859,
Rattus norvegicus	ENSRNOG00000007234	1 retrocopy	retro_rnor_2379,
Tarsius syrichta	ENSTSYG00000014341	1 retrocopy	retro_tsyr_1008,