RetrogeneDB ID: retro_mdom_1255

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:118481950..118483301(+)
• Located in intron of: ENSMODG00000000193

Retrocopy information

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

Parental gene information

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

Sequence

>retro_mdom_1255
CCTGCCCAGAGCGGAGATATGAGCAGCTGCAGGAGGGACGCCAATGAGGAGTTCAACGAACAGCTGAGGCTCCAGCAGCT
CCAAGAGGAGGCCAAGCTCTCGGCCAGCGGCTTGCCCGAGGGCGATGACCCTTACACTTTTGTGGACCCGGCGGATGGCA
CCACCTAAGAATGGGATCGAGACAAGAAGGCATGGTTCTTTAAGATTATGGAGGATTTCCTTGCCAATTACCAGGCCAAT
TATGGGTTCCCTGCTGATAGCTCCTCTTCTTCTGGTGGGCAGAAAGAGAAGCAGGCTGATGTGGAAGTAAAAGCTTCACA
AAAACCTATAGATCCAAAAGCCTCACAAAACCCTGAAAAGAAACAGAAAGGTGAAAAAAGAAAGCCTGAGCCTGGGTGGT
TTCATGTCGAGGAAGACAAAAATACAAATGTGTATGTGACTGGCTTACCTCCAGACATCACAAAAGATGAATTTGTACAG
CTCATGTCCAAGTGTGGCATCATCATGAGAGACCCACAGACAGAAGAATATAAAATTAAGCTTTATAAAGACAAACAAGG
AAATCTTAAAGGAGATGGACTTTGCTGTTATCTGAAGAGGGAGTCTGTGGATCTAGCATTAAGACTTCTGGATGATGATG
AAATCAGAGGCTATAAACTGCATGTAGAAATGGCAAAATTTCAGCTAAAAGGAGAATATGATGCCAGCAAAAAAGAAGAA
GAAATGCAAAGACTACAGGAAAAAGATGTCTCAGCAACAAAAACAACTGGATTGGCGGCCTGAAAAGAAAGCCAACACTG
CTCAAATGCGGCACGAGCGGGTGGTTATTATCAGGAATATGTTCCACCCGAAGGATTTTGAGGCAGATCCACTGGTACTA
AATGAGATCCAGGAAGACCTCCGATCAGAGTGTGAAAAGTTTGGGCAAGTTAAGAAAGTCCTTGTCTTTGACCGACACCC
AGATGGAGTGGCCTCAGTGTCCTACAAAGAACCAGAAGAAGCTGACCTATGTATACAAGCCCTCAATGGGAGGTGGTTTG
GCGGTCGTCAGTTAAACGTGGAAGTGTTGGATGGTGTGATTGATTTTCAGGTGGAGGAGACATCCAGAGAGAGGGAAGAA
AGACCGAAAGGTTGGGAGTCTTTTTTAGAGCATCATAACAAACAAAAAGAAACCGATTCTGCTGATCCAAATTCTGCTTC
CGGAAGTGTGGCCCTGGCAAAAGGGAAATCATCCTCAGCGGATATGACCTCACCTGGAGCAAAGGAGGAAGCTGGTAATG
GGGAATGCAGTAGAGGAGGGACCCAAACTAAGGACAGCAACTTGGGCCTCGGTGATAATCAAGTCCAGGGA

Alignment

ORF - retro_mdom_1255 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAQEREDMSGNQHDNNEEFTEQLRLQQLYEEC----SELPEGNDPYTYVDQADGTAYEWDLDKKAWFPKI
          PAQ...DMS....D.NEEF.EQLRLQQL.EE.....S.LPEG.DPYT.VD.ADGT..EWD.DKKAWF.KI
Retrocopy PAQSG-DMSSCRRDANEEFNEQLRLQQLQEEAKLSASGLPEGDDPYTFVDPADGTT*EWDRDKKAWFFKI

Parental  TEDFLATYQANYGFPPDEPASSHPQKAKESDKNVKAGEDPTDQKTAQNSEKKQKGEKRKPEPGWFHVEEG
          .EDFLA.YQANYGFP.D...SS..QK.K..D..VKA...P.D.K..QN.EKKQKGEKRKPEPGWFHVEE.
Retrocopy MEDFLANYQANYGFPADSSSSSGGQKEKQADVEVKASQKPIDPKASQNPEKKQKGEKRKPEPGWFHVEED

Parental  RNTNVYVTGLPPDITKDEFIQLMSKCGIIMKDPQTEEYKIKLYKDKQGNLKGDGLCCYLKKESVDLALKL
          .NTNVYVTGLPPDITKDEF.QLMSKCGIIM.DPQTEEYKIKLYKDKQGNLKGDGLCCYLK.ESVDLAL.L
Retrocopy KNTNVYVTGLPPDITKDEFVQLMSKCGIIMRDPQTEEYKIKLYKDKQGNLKGDGLCCYLKRESVDLALRL

Parental  LDDDVIRGYKLHVEKAKFQLKGEYDAS-KKKKKCKDYRKKLSLQQKQLDWRPEKKAGSTRMRHERVVVIR
          LDDD.IRGYKLHVE.AKFQLKGEYDAS.KKKKKCKDYRKK.S.QQKQLDWRPEKKA....MRHERVV.IR
Retrocopy LDDDEIRGYKLHVEMAKFQLKGEYDAS>KKKKKCKDYRKKMSQQQKQLDWRPEKKANTAQMRHERVVIIR

Parental  NMFHPKDFEEDPLVLNEIREDLRTECEKFGQVKKVLLFDRHPDGVASVSYKEPEEADLCIQALNGRWFGG
          NMFHPKDFE.DPLVLNEI.EDLR.ECEKFGQVKKVL.FDRHPDGVASVSYKEPEEADLCIQALNGRWFGG
Retrocopy NMFHPKDFEADPLVLNEIQEDLRSECEKFGQVKKVLVFDRHPDGVASVSYKEPEEADLCIQALNGRWFGG

Parental  RQLHVEVWDGVTDYQVEETSREREERLKGWESFLENPNTQKETHLFDPDSASGSMPLTAGKQSPENNAPK
          RQL.VEV.DGV.D.QVEETSREREER.KGWESFLE..N.QKET...DP.SASGS..L..GK.S.......
Retrocopy RQLNVEVLDGVIDFQVEETSREREERPKGWESFLEHHNKQKETDSADPNSASGSVALAKGKSSSADMTSP

Parental  GPTKEEVNNGESFNEDEAQSTDSSLGDSDNEDTG
          G..KEE..NGE.......Q..DS.LG..DN...G
Retrocopy G-AKEEAGNGEC-SRGGTQTKDSNLGLGDNQVQG

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_1255 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1255 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,