RetrogeneDB ID: retro_mdom_629

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:581255621..581256515(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000009807
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019662
• Aliases: None
• Description: None

Sequence

>retro_mdom_629
TTTAACAATAGGAGCCAGGATGATCAAGTTGAAGAACCCCAGCTGTCAGATTGGTTTAATCCCAAAAAACGCCCTGATGT
TCTGACTGTGACAGATTGGCTTGCTCCAGTTGTGTGGGAGGGGACTTACCATAGGAAGATCCTGGAAGACTATTACACAA
AGCAAAAGATCACAGTGGGCTTAACAGTATTTGCTGTTGGAAGATATCTCGATCGGTATTTGGAGGAGTTCATGATGTCT
GCTGAAAAATACTTCATGGTTGGTCAAAGAGTCATATTTTACATCATGGTGGATGACTCCTCTAAGATTCCTTGGATACA
GCTGGGTTCCCTTCGTACACTGAAAGTATTTGAAATCAACAGAGAAAAGAGGTGGCAGGACATAAGTATGATGCGCATGA
AGATCATTGGGGAGCACATTATACATCACATCCAATATGAAGTTGATTTCCTCTTTTGCATGGATGTGGATCAGATCTTC
AAGGATGATTTTGGAGTAGAGACTCTAGGCGAGTCAGTAGCTCAACTCCAGGCATGGTGGTATAAGGTAGATCCCACTGA
GTTCACTTATGAGAGAAGACCTGAGTCTGCGGCATACATCCCTTTTGGCCAGGGAGATTTCTATTACCATGCAGCCATTT
TTGGGGGCACACCCCTTAGGGTTTGGAACCTCACCCAGGAATGCTTCAAGGGAATTCTTCAAGACAAGGAAAATGACATT
GAAGCTGAGTGGCATGATGAAAGCCATCTCAACAAGTATTTCCTTCTCAACAAACCCACAAAAATCTTATCCCCAGAATA
CTGCTGGGATTATCATATAGGCTCCTCCTCAGATATAAGACTTGTCAAAATTGCTTGGCAGTCAAAAGAATATAATGTCG
TTAGAAGTAACCCC

Alignment

ORF - retro_mdom_629 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.32 %
• Parental protein coverage: 81.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FALRSQDDQVEEPQLSDWFNPKKRPDVLTVTDWLAPVVWEGTYHRKILEDYYTKQKITVGLTVFAVGRYL
          F..RSQDDQVEEPQLSDWFNPKKRPDVLTVTDWLAPVVWEGTYHRKILEDYYTKQKITVGLTVFAVGRYL
Retrocopy FNNRSQDDQVEEPQLSDWFNPKKRPDVLTVTDWLAPVVWEGTYHRKILEDYYTKQKITVGLTVFAVGRYL

Parental  DRYLEEFMTSAEKYFMVGQRVIFYIMVDDSSKIPWIQLGSLRTLKVFEINREKRWQDISMMRMKIIGEHI
          DRYLEEFM.SAEKYFMVGQRVIFYIMVDDSSKIPWIQLGSLRTLKVFEINREKRWQDISMMRMKIIGEHI
Retrocopy DRYLEEFMMSAEKYFMVGQRVIFYIMVDDSSKIPWIQLGSLRTLKVFEINREKRWQDISMMRMKIIGEHI

Parental  IHHIQYEVDFLFCMDVDQIFKDDFGVETLGESVAQLQAWWYKADPTEFTYERRPESAAYIPFGQGDFYYH
          IHHIQYEVDFLFCMDVDQIFKDDFGVETLGESVAQLQAWWYK.DPTEFTYERRPESAAYIPFGQGDFYYH
Retrocopy IHHIQYEVDFLFCMDVDQIFKDDFGVETLGESVAQLQAWWYKVDPTEFTYERRPESAAYIPFGQGDFYYH

Parental  AAIFGGTPLRVLNLTQECFKGILQDKENDIEAEWHDESHLNKYFLLNKPTKILSPEYCWDYHIGSSSDIR
          AAIFGGTPLRV.NLTQECFKGILQDKENDIEAEWHDESHLNKYFLLNKPTKILSPEYCWDYHIGSSSDIR
Retrocopy AAIFGGTPLRVWNLTQECFKGILQDKENDIEAEWHDESHLNKYFLLNKPTKILSPEYCWDYHIGSSSDIR

Parental  LVKIAWQSKEYNVVRSNP
          LVKIAWQSKEYNVVRSNP
Retrocopy LVKIAWQSKEYNVVRSNP

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	1.19 RPM	4.53 RPM
SRP007412_cerebellum	0.65 RPM	2.61 RPM
SRP007412_heart	5.98 RPM	25.72 RPM
SRP007412_kidney	7.90 RPM	27.65 RPM
SRP007412_liver	2.52 RPM	13.09 RPM
SRP007412_testis	0.39 RPM	3.14 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_629 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_629 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000019662	1 retrocopy	retro_mdom_629 ,
Mustela putorius furo	ENSMPUG00000007373	1 retrocopy	retro_mputfur_307,