RetrogeneDB ID: retro_mdom_1910

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 8:78973772..78974239(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000004426
• Aliases: None
• Description: None

Sequence

>retro_mdom_1910
TACTTATCAGGATCTGAGCTCAGTGAAGCCATGAACCAGGAGACCAACCAGAAGTGGGTACCCCTTCTGTGCACTGCAAG
TTTCTATGGAAACCCTTGAACCAATGGCATGTGCTCTGCTACTAAAAGGATTTCCTTCAAAGGCAGCAAAATGGTGGGAG
AATAAACCCTAAGTAGATAGCAGCCCCATTGCTGCTGCCCTAGAAAACTTCAGTTCAGCATGTGAAGAGGAGGTGGACTT
TACGCCTGATGATAGCTTAGCCAGATTCTCTCAGATGCCTGCGCCCATCAGATGACAGCTATGAACATATTTAAAGATGA
CAGTCTAGGCAAGACAGTTACATCTAGTCAGATGAAGCCTTCTCCACAACTCTCTCAACAGGTTCTCTTCTGGAGACATA
TCAGAGCTCCTCTGAGGAAGGGAAGTTGTCTGAGAAATCCAAACTGAGAGGCATTCACTGCTCAGCA

Alignment

ORF - retro_mdom_1910 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.15 %
• Parental protein coverage: 65.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  YTNRAELSTAMAQETNQTQVPLLCTTGCGFYGNPRTNGMCSVCY-KDFLQRQQNSGRISPS-VASSPSPA
          Y....ELS.AM.QETNQ..VPLLCT....FYGNP.TNGMCS....KDFLQRQQN.GRI.P..V.SSP..A
Retrocopy YLSGSELSEAMNQETNQKWVPLLCT--ASFYGNP*TNGMCSATK<KDFLQRQQNGGRINPK<VDSSPIAA

Parental  ALETFPVAYAEEADPTPDDVLARSSSQTPV-THQMTAMSISKEDSQSKTVSYAQ-SDEAISTTPSSGSLL
          ALE.F..A..EE.D.TPDD.LAR..SQ.P...HQMTAM.I.K.DS..KTV...Q.......T......L.
Retrocopy ALENFSSACEEEVDFTPDDSLAR-FSQMPA<AHQMTAMNIFKDDSLGKTVTSSQ<DEAFSTTLSTGSLLE

Parental  ETSQSSSEEEKSSEKSKPKKNRCFA
          ....SS.E..K.SEKSK.....C.A
Retrocopy TYQSSSEE-GKLSEKSKLRGIHCSA

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_1910 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1910 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002366	2 retrocopies	retro_chof_1050, retro_chof_1846,
Cavia porcellus	ENSCPOG00000005076	2 retrocopies	retro_cpor_1398, retro_cpor_774,
Felis catus	ENSFCAG00000027317	1 retrocopy	retro_fcat_641,
Homo sapiens	ENSG00000107372	1 retrocopy	retro_hsap_2063,
Gorilla gorilla	ENSGGOG00000008957	1 retrocopy	retro_ggor_1485,
Myotis lucifugus	ENSMLUG00000007173	2 retrocopies	retro_mluc_1233, retro_mluc_1993,
Monodelphis domestica	ENSMODG00000004426	1 retrocopy	retro_mdom_1910 ,
Monodelphis domestica	ENSMODG00000019428	1 retrocopy	retro_mdom_685,
Mustela putorius furo	ENSMPUG00000008951	1 retrocopy	retro_mputfur_143,
Mus musculus	ENSMUSG00000024750	1 retrocopy	retro_mmus_1176,
Oryctolagus cuniculus	ENSOCUG00000000795	1 retrocopy	retro_ocun_1546,
Procavia capensis	ENSPCAG00000007436	1 retrocopy	retro_pcap_112,
Pongo abelii	ENSPPYG00000019290	1 retrocopy	retro_pabe_1676,
Vicugna pacos	ENSVPAG00000000700	1 retrocopy	retro_vpac_23,