RetrogeneDB ID: retro_mdom_1259

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:151315448..151315967(+)
• Located in intron of: ENSMODG00000003553

Retrocopy information

• Ensembl ID: ENSMODG00000003546
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011614
• Aliases: None
• Description: None

Sequence

>retro_mdom_1259
AACTTCCGCGTGGCCAAGGTGTCCCGGGAGAACTCGGACAAGATCAACTGCTTCGATTTCAGCCCCAATGGCGAGACGGT
CATCTCCAGCAGCGAGGACGACTCCATCGTCCTGTACGACTGTCAGGAGGGCAAACCAAAGCAAACACTGTACAGTAAGA
AGTATGGAGTGGACCTAATCAGATACACCCATGCAGCCAACACCGTAGTGTACAGTTCTAACAAAATAGACGATACAATC
TGCTACCTGTCCTGGCACGATAACAAATACATCCGGGACTTCCCAGGACACAAGAGGGTGGTAGCCTTGTCCATGTCACC
AATAGATGATGCTTTTATCTCTGGGTCCCTGGATAAAACCATCCGGCTCTGGGATCTTCGGTCTCCTAACTGCCAGGGTC
TCATGCATCTCCAAGGAAAACCAGTTTGTTCTTTTGATCCAGAAGCGTTAATTTTTGCTGCTGGAGTCCATTCTGAAATG
GCTAAACTTGATGACCTTCCTTCTTTTGATAAGGGGCCA

Alignment

ORF - retro_mdom_1259 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 55.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SFRVAKVFRENSDKINCFDFSPNGETVISSSDDDSIVLYDCQEGKPKRTLYSKKYGVDLIRYTHAANTVV
          .FRVAKV.RENSDKINCFDFSPNGETVISSS.DDSIVLYDCQEGKPK.TLYSKKYGVDLIRYTHAANTVV
Retrocopy NFRVAKVSRENSDKINCFDFSPNGETVISSSEDDSIVLYDCQEGKPKQTLYSKKYGVDLIRYTHAANTVV

Parental  YSSNKIDDTIRYLSLHDNKYIRYFPGHNKRVVALSMSPIDDTFISGSLDKTIRLWDLRSPNCQGLMHLQG
          YSSNKIDDTI.YLS.HDNKYIR.FPGH.KRVVALSMSPIDD.FISGSLDKTIRLWDLRSPNCQGLMHLQG
Retrocopy YSSNKIDDTICYLSWHDNKYIRDFPGH-KRVVALSMSPIDDAFISGSLDKTIRLWDLRSPNCQGLMHLQG

Parental  KPVCSFDPEGLIFAAGVNSEMVKLYDLRSFDKGP
          KPVCSFDPE.LIFAAGV.SEM.KL.DL.SFDKGP
Retrocopy KPVCSFDPEALIFAAGVHSEMAKLDDLPSFDKGP

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_1259 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1259 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000774	1 retrocopy	retro_chof_2299,
Callithrix jacchus	ENSCJAG00000006114	1 retrocopy	retro_cjac_3022,
Homo sapiens	ENSG00000164091	2 retrocopies	retro_hsap_2816, retro_hsap_419,
Loxodonta africana	ENSLAFG00000028309	1 retrocopy	retro_lafr_639,
Macropus eugenii	ENSMEUG00000009280	1 retrocopy	retro_meug_1207,
Macaca mulatta	ENSMMUG00000008234	2 retrocopies	retro_mmul_339, retro_mmul_511,
Monodelphis domestica	ENSMODG00000011614	4 retrocopies	retro_mdom_1259 , retro_mdom_144, retro_mdom_219, retro_mdom_398,
Nomascus leucogenys	ENSNLEG00000007104	2 retrocopies	retro_nleu_1016, retro_nleu_1195,
Otolemur garnettii	ENSOGAG00000016032	1 retrocopy	retro_ogar_1314,
Pongo abelii	ENSPPYG00000013812	2 retrocopies	retro_pabe_185, retro_pabe_300,
Rattus norvegicus	ENSRNOG00000048441	3 retrocopies	retro_rnor_1003, retro_rnor_1109, retro_rnor_1152,