RetrogeneDB ID: retro_mdom_1703

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:913339..913894(+)
• Located in intron of: ENSMODG00000016811

Retrocopy information

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

Parental gene information

• Parental gene symbol: UCP2
• Ensembl ID: ENSMODG00000007498
• Aliases: None
• Description: uncoupling protein 2 (mitochondrial, proton carrier) [Source:HGNC Symbol;Acc:12518]

Sequence

>retro_mdom_1703
TCTGTCAAGCAATTCTACACCAACGGGTCTGAACATGCAGATATTGGAAGTCGCCTCCTGGCAGGCTGTACCACAGGAGC
ACTGGTAGTATGTGTAACCCAATGCATAGATGTGATAAAGGTATGTTTACAGGCCAAGGCTCTTGCAGGGCGCAGCTGGA
GATAACAGGGTGCAGTGCATGCCTATACGACTATCACCTGAGAGGAGGGACTTTGGGGCCTATGGAAAGGAACTTTGTCC
AATGTTGCTCGCGATGCTATTGTCAACTGTGCTGAGCTAGTGATCCATGACCTCATCAGAGATGCCATCCTGAAGGCCCA
CTTCAAGACTGATGACCTTGTATGACCCTTCACTTTAGCCTTTGGGCCTGGCTTCTACACCACCATCATCACCTCCCCTG
TGGATGCGGTCAAGATGAGATACATGAACTCTGCCTCGAGCCGGTATGCCAGTGGAGGCCACTGTACTCTTGCTATGCTT
TAGAAAGAAGGGCCCTAACTTTTCTACAAAGGGTTCATGCCTTCCTTCCTCCACTTGGGCTCCTGGAATATAGTG

Alignment

ORF - retro_mdom_1703 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.97 %
• Parental protein coverage: 58.73 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVKQFYTKGSEHAGIGSRLLAGCTTGALAVGVAQPTDVVKVRFQAQARAGGSRRYQGTMDAYKTIAREEG
          SVKQFYT.GSEHA.IGSRLLAGCTTGAL.V.V.Q..DV.KV..QA.A.AG.S.R.QG...AY.TI..EEG
Retrocopy SVKQFYTNGSEHADIGSRLLAGCTTGALVVCVTQCIDVIKVCLQAKALAGRSWR*QGAVHAYTTIT*EEG

Parental  LRGLWKGTSPNVARNAIVNCAELVTYDLIKDALLKAHLMTDDLPCHFTSAFGAGFCTTIIASPVDVVKTR
          L.GLWKGT..NVAR.AIVNCAELV..DLI.DA.LKAH..TDDL...FT.AFG.GF.TTII.SPVD.VK.R
Retrocopy LWGLWKGTLSNVARDAIVNCAELVIHDLIRDAILKAHFKTDDLV*PFTLAFGPGFYTTIITSPVDAVKMR

Parental  YMNSASGQYASAGHCALTMLRKEGPQAFYKGFMPSFLRLGSWNVV
          YMNSAS..YAS.GHC.L.ML.KEGP..FYKGFMPSFL.LGSWN.V
Retrocopy YMNSASSRYASGGHCTLAML*KEGP*LFYKGFMPSFLHLGSWNIV

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_1703 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1703 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000014773	1 retrocopy	retro_etel_2156,
Macropus eugenii	ENSMEUG00000011481	2 retrocopies	retro_meug_2102, retro_meug_505,
Monodelphis domestica	ENSMODG00000007498	2 retrocopies	retro_mdom_1122, retro_mdom_1703 ,
Otolemur garnettii	ENSOGAG00000001700	1 retrocopy	retro_ogar_601,