RetrogeneDB ID: retro_mdom_1854

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:114343549..114344413(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000018305
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CASP6
• Ensembl ID: ENSMODG00000005948
• Aliases: None
• Description: caspase 6, apoptosis-related cysteine peptidase [Source:HGNC Symbol;Acc:1507]

Sequence

>retro_mdom_1854
GGCAGGGACTTCTCGGCCCCAGGAGATGCTGAGCAGAATGCAACAGAAATAGACGCCTTCTTTAAAAGCAAACCCCTGGA
CCCAGCAGAACAGTACAAGATGGACCACAAGAGGAGAGGCGTGGCTTTGATCTTCAACCACGAGCGCTTCTTCTGGCACC
TGACCTTGCCTGAGAGACGGGGCACACGGGCCGACAGGGACAACCTGCGGCAGAGGCTCTCGGATCTGGGCTTCGAAGTG
AATTGCTTTGATGACCTCAAAGCCGAAGACCTGCTGATGACCATTCATATGGTGTCCACCTCTAGCCACATAGATGCCGA
TTGCTTCCTGTGTGTGTTCCTGACACACGGGGAAGGAAACCACATCTACGCCTACGATGCCAAAATCGATATCCAGAAGC
TGACCGCCATGTTTAAAGGAGACAAATGCCAGACCTTGGTTGGGAAACCCAAGATATTTGTCATCCAGGCCTGTCGAGGA
GACCAGCACGATATTCCGGTCATTCCTCTGGACGTGGTCGACCATCTGTCGGACAAGGTGGACGTCAATGAAACAGAAGT
GGACGCTGCCTCCGTTTATACCCTCCCGGCTGGAGCTGACTTCCTCATGTGCTATTCAGTGGCAGAAGGTTATTACTCTC
ACCGGGAGACAGTGCATGGTTCCTGGTACATTCAGGATTTGTGTGAGATGCTGGAAAAATACGGCTCCTCCTTAGAGTTT
ACGGAACTCCTTACCCTGGTGAATAGGAAAGTTTCCCAGCGCAGAGTGGACTTCTGCAAGGACCCCAACGCCATTGGGAA
AAAGCAGGTCCCTTGTTTTGCCTCCATGCTGACCAAAAAGCTCTATCTCTTTCCAAAGCCTAAG

Alignment

ORF - retro_mdom_1854 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.26 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLFFVFEGDAEQNATEIDAFFKSKPLDPAEQYKMDHKRRGVALIFNHERFFWHLTLPERRGTRADRDNLR
          G..F...GDAEQNATEIDAFFKSKPLDPAEQYKMDHKRRGVALIFNHERFFWHLTLPERRGTRADRDNLR
Retrocopy GRDFSAPGDAEQNATEIDAFFKSKPLDPAEQYKMDHKRRGVALIFNHERFFWHLTLPERRGTRADRDNLR

Parental  QRLSDLGFEVNCFDDLKAEDLLMTIHMVSTSSHIDADCFLCVFLTHGEGNHIYAYDAKIDIQKLTAMFKG
          QRLSDLGFEVNCFDDLKAEDLLMTIHMVSTSSHIDADCFLCVFLTHGEGNHIYAYDAKIDIQKLTAMFKG
Retrocopy QRLSDLGFEVNCFDDLKAEDLLMTIHMVSTSSHIDADCFLCVFLTHGEGNHIYAYDAKIDIQKLTAMFKG

Parental  DKCQTLVGKPKIFVIQACRGDQHDIPVIPLDVVDHLSDKVDVNETEVDAASVYTLPAGADFLMCYSVAEG
          DKCQTLVGKPKIFVIQACRGDQHDIPVIPLDVVDHLSDKVDVNETEVDAASVYTLPAGADFLMCYSVAEG
Retrocopy DKCQTLVGKPKIFVIQACRGDQHDIPVIPLDVVDHLSDKVDVNETEVDAASVYTLPAGADFLMCYSVAEG

Parental  YYSHRETVHGSWYIQDLCEMLEKYGSSLEFTELLTLVNRKVSQRRVDFCKDPNAIGKKQVPCFASMLTKK
          YYSHRETVHGSWYIQDLCEMLEKYGSSLEFTELLTLVNRKVSQRRVDFCKDPNAIGKKQVPCFASMLTKK
Retrocopy YYSHRETVHGSWYIQDLCEMLEKYGSSLEFTELLTLVNRKVSQRRVDFCKDPNAIGKKQVPCFASMLTKK

Parental  LYLFPKPK
          LYLFPKPK
Retrocopy LYLFPKPK

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_1854 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1854 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
Loxodonta africana	ENSLAFG00000002727	1 retrocopy	retro_lafr_291,
Microcebus murinus	ENSMICG00000010297	2 retrocopies	retro_mmur_709, retro_mmur_844,
Monodelphis domestica	ENSMODG00000005948	1 retrocopy	retro_mdom_1854 ,
Vicugna pacos	ENSVPAG00000009840	1 retrocopy	retro_vpac_431,