RetrogeneDB ID: retro_mdom_193

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:454862305..454863055(-)
• Located in intron of: ENSMODG00000006491

Retrocopy information

• Ensembl ID: ENSMODG00000000199
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000014087
• Aliases: None
• Description: None

Sequence

>retro_mdom_193
ATGAGCAGCTGCAGGCGGGACGCCAATGAGGAGTTTAACGAACAGCTGAGGCTCCAGCAGCTCCAAGAGGAGGCCAAGCT
CTCGGCCAGCGGCTCGCCCGAGGGCCCCGAGGGCGATGACCCTTACACTTTCGTGGACCCGGCGGATGGCACCGCCTACG
AATGGGATCGAGACAAGAAGGCATGGTTCCCTAAGATTACGGAGGATTTCCTTGCCAATTATCAGGCCAATTATGGGTTC
CCTGCTGATAGCTCCTCTTCTTCCGGTGGGCAGAAAGAGAAGCAGGCTGATGTGGAGGTAAAAGCTTCGCAAAAACCTAC
AGATCCAAAAGCCTCACAAAACCCTGAAAAGAAACAGAAAGGTGAAAAAAGAAAGCCTGAGCCTGGGTGGTTTCATGTCG
AGGAAGACAAAAATACAAATGTGTATGTGACTGGCTTACCTCCAGACATCACAAAAGATGAATTTGTACAGCTCATGTCC
AAATGTGGCATCATCATGAGAGACCCACAGACAGAAGAATATAAAATTAAGCTTTATAAAGACAAACAAGGAAATCTTAA
AGGAGATGGACTTTGCTGTTATCTGAAGAGGGAGTCTGTGGATCTAGCATTAAGACTTCTGGATGATGATGAAATCAGAG
GCTATAAACTGCATGTAGAAATGGCAAAATTTCAGCTAAAAGGAGAATATGATGCTAGCAAAAAGAAGAAGAAATGCAAA
GACTACAGGAAAAAGATGTCTCAGCAACAA

Alignment

ORF - retro_mdom_193 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 53.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGNQHDNNEEFTEQLRLQQLYEE----CSELPEG---NDPYTYVDQADGTAYEWDLDKKAWFPKITEDF
          MS....D.NEEF.EQLRLQQL.EE.....S..PEG....DPYT.VD.ADGTAYEWD.DKKAWFPKITEDF
Retrocopy MSSCRRDANEEFNEQLRLQQLQEEAKLSASGSPEGPEGDDPYTFVDPADGTAYEWDRDKKAWFPKITEDF

Parental  LATYQANYGFPPDEPASSHPQKAKESDKNVKAGEDPTDQKTAQNSEKKQKGEKRKPEPGWFHVEEGRNTN
          LA.YQANYGFP.D...SS..QK.K..D..VKA...PTD.K..QN.EKKQKGEKRKPEPGWFHVEE..NTN
Retrocopy LANYQANYGFPADSSSSSGGQKEKQADVEVKASQKPTDPKASQNPEKKQKGEKRKPEPGWFHVEEDKNTN

Parental  VYVTGLPPDITKDEFIQLMSKCGIIMKDPQTEEYKIKLYKDKQGNLKGDGLCCYLKKESVDLALKLLDDD
          VYVTGLPPDITKDEF.QLMSKCGIIM.DPQTEEYKIKLYKDKQGNLKGDGLCCYLK.ESVDLAL.LLDDD
Retrocopy VYVTGLPPDITKDEFVQLMSKCGIIMRDPQTEEYKIKLYKDKQGNLKGDGLCCYLKRESVDLALRLLDDD

Parental  VIRGYKLHVEKAKFQLKGEYDASKKKKKCKDYRKKLSLQQ
          .IRGYKLHVE.AKFQLKGEYDASKKKKKCKDYRKK.S.QQ
Retrocopy EIRGYKLHVEMAKFQLKGEYDASKKKKKCKDYRKKMSQQQ

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	29.44 RPM	0.00 RPM
SRP007412_cerebellum	28.08 RPM	0.00 RPM
SRP007412_heart	21.53 RPM	0.00 RPM
SRP007412_kidney	21.07 RPM	0.00 RPM
SRP007412_liver	18.13 RPM	0.00 RPM
SRP007412_testis	5.50 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_193 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_193 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000009234	1 retrocopy	retro_mluc_352,
Monodelphis domestica	ENSMODG00000014087	3 retrocopies	retro_mdom_1255, retro_mdom_1891, retro_mdom_193 ,