RetrogeneDB ID: retro_mdom_297

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:5692188..5693286(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000012163
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: METAP2
• Ensembl ID: ENSMODG00000008173
• Aliases: None
• Description: methionyl aminopeptidase 2 [Source:HGNC Symbol;Acc:16672]

Sequence

>retro_mdom_297
ACAGTGCCACCCTCAGTGCCCATATGTGACCTGTATCCCAGTGGTGTGTTTCCAAAGGGCCAAGAGTGCGAGTACCCCTC
AACACAAGATGGGCGAACAGCAGCTTGGAGAAGCACAAATGAAGAAAAGAAAGCGCTAGACCAAGCCAGTGAGGAAATCT
GGAATGATTTTCGGGAAGCTGCCGAGGCACACCGACAAGTAAGGAAGTATGTGATGAGCTGGATCAAGCCTGGGATGACC
ATGATCGAGATCTGTGAAAAACTGGAAGATTGTTCCCATAAGCTAATAAAAGAGAATGGCCTAAATGCAGGACTTGCCTT
CCCTACAGGCTGCTCCCTCAATAACTGTGCAGCCCATTACACTCCCAATGCTGGAGACCCCACAGTCTTGCAATATGATG
ATATCTGCAAGATAGATTTTGGAACACACATCAGTGGTAGGATTATTGATTGTGCTTTTACTGTCACTTTCAACCCCAAA
TATGACACATTGTTAAAGGCTGTAAAAGATGCTACTAATACTGGAATAAAGTGTGCTGGAATTGATGTTCGCCTTTGTGA
TGTTGGTGAGGCCATTCAGGAAGTTATGGAATCTTATGAGGTTGAAATTGATGGCAAAACATATCAAGTGAAACCCATTC
GAAATCTTAACGGGCATTCAATTGGGCCATATAGAATACATGCTGGGAAAACGGTGCCCATTGTCAAAGGAGGAGAAGCA
ACAAGAATGGAGGAAGGAGAAGTATATGCCATAGAGACCTTTGGCAGTACAGGGAAAGGTGTGGTACATGACGATATGGA
ATGTTCGCATTATATGAAAAATTTTGATGTTGGACATGTGCCAATAAGACTTCCAAGAGCAAAACATTTGTTAAATGTCA
TCAATGAAAACTTTGGTACTCTGGCCTTCTGCCGCAGGTGGCTAGATCGCCTAGGAGAAAGCAAATACCTGATGGCTCTC
AAGAATCTGTGTGACTTGGGCATTGTGGATCCCTATCCTCCCTTATGTGACATCAAAGGCTCCTACACAGCACAATTTGA
GCACACCATCCTCTTACGCCCAACATGCAAAGAAGTTGTCAGCAGAGGAGACGACTAT

Alignment

ORF - retro_mdom_297 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.18 %
• Parental protein coverage: 75.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TDPPSVPICDLYPSGVFPKGQECEYPSTQDGRTAAWRSTNEEKKALDQASEEIWNDFREAAEAHRQVRKY
          T.PPSVPICDLYPSGVFPKGQECEYPSTQDGRTAAWRSTNEEKKALDQASEEIWNDFREAAEAHRQVRKY
Retrocopy TVPPSVPICDLYPSGVFPKGQECEYPSTQDGRTAAWRSTNEEKKALDQASEEIWNDFREAAEAHRQVRKY

Parental  VMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDPTVLQYDDICKIDF
          VMSWIKPGMTMIEICEKLEDCS.KLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDPTVLQYDDICKIDF
Retrocopy VMSWIKPGMTMIEICEKLEDCSHKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDPTVLQYDDICKIDF

Parental  GTHISGEIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQV
          GTHISG.IIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQV
Retrocopy GTHISGRIIDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDGKTYQV

Parental  KPIRNLNGHSIGPYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHV
          KPIRNLNGHSIGPYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHV
Retrocopy KPIRNLNGHSIGPYRIHAGKTVPIVKGGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMKNFDVGHV

Parental  PIRLPRAKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTI
          PIRLPRAKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTI
Retrocopy PIRLPRAKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTI

Parental  LLRPTCKEVVSRGDDY
          LLRPTCKEVVSRGDDY
Retrocopy LLRPTCKEVVSRGDDY

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	15.85 RPM	0.00 RPM
SRP007412_cerebellum	17.63 RPM	0.00 RPM
SRP007412_heart	22.13 RPM	0.00 RPM
SRP007412_kidney	23.70 RPM	0.00 RPM
SRP007412_liver	24.17 RPM	0.00 RPM
SRP007412_testis	39.09 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_297 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_297 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006353	1 retrocopy	retro_cfam_1330,
Monodelphis domestica	ENSMODG00000008173	1 retrocopy	retro_mdom_297 ,
Mus musculus	ENSMUSG00000036112	2 retrocopies	retro_mmus_3689, retro_mmus_770,
Otolemur garnettii	ENSOGAG00000008469	1 retrocopy	retro_ogar_2163,
Rattus norvegicus	ENSRNOG00000021881	2 retrocopies	retro_rnor_1707, retro_rnor_547,