RetrogeneDB ID: retro_mdom_1808

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:188429746..188430337(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000015991
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SLC25A17
• Ensembl ID: ENSMODG00000013036
• Aliases: None
• Description: solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17 [Source:HGNC Symbol;Acc:10987]

Sequence

>retro_mdom_1808
AGAAGTGGAAATTCTTTATACATAGTACTGATGGAGATCATTAAAGAATAAAGACTCTTGGCACCATAACAAGGGGGTTT
CCTGTCATCTTCAGCTTTTGCTGCTCAAATTTTGTCTATTCCTACACTTTTAATAGCTTCAAAGATGTCTGGATCAAAGT
TCAACATTCTATTACCAGAAAGGCTTTGGTCATTGGATTTGTTGCAGATGTGATGAATGTGCTGCTGACCCTACTGCTGT
GGATAGTGAACATCCAGATAGCCCAGGGGGCCAAGTTCAGAAATGAAGACATGGCATCCACCAACTATAAGGGCATCTTA
AAAGCCTTCCTCAAATCATGCCCGGTGAAGGAGCCCTTCCTCTTTGGACTAGTACGCTTCCTGCCCCATTGCTGGTCTTC
ATCTTGGCCATCCGTTTCATGTCCTAGGAATGCTCAAGGGACAACTCTTGAAGAAGCAGGCACAGCTTTCTTCTCTGAAT
GTGTTTGTTACTGGGGCCATTGGCAAGGCTATCGCCACCAGAGTCATCTATCTGATGCAAACGGTGCAGTACATTCTGAG
GTTTGGGTGTCATAGGCTGAAGTCTGAAAAC

Alignment

ORF - retro_mdom_1808 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.33 %
• Parental protein coverage: 64.82 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RKSKTTHTVLMEIIKEEGLLAPYRGWF-PVISSLCCSNFVYFYTFNSLKAVWVKGQHSTTGKDLVVGFVA
          R.......VLMEIIKE..LLAP..G.F.PVI.S.CCSNFVY.YTFNS.K.VW.K.QHS.T.K.LV.GFVA
Retrocopy RSGNSLYIVLMEIIKE*RLLAP*QGGF<PVIFSFCCSNFVYSYTFNSFKDVWIKVQHSITRKALVIGFVA

Parental  GVVNVLLTTPLWVVNTRLKLQGAKFRNEDIVPTNYKGILDAF-HQIMRDEGVLALWNGTLPSLLLVFNPA
          .V.NVLLT..LW.VN.....QGAKFRNED...TNYKGIL.AF..QIM..EG.L.LW..TLP..LLVF..A
Retrocopy DVMNVLLTLLLWIVNIQI-AQGAKFRNEDMASTNYKGILKAF<PQIMPGEGALPLWTSTLPAPLLVFILA

Parental  IQFMFYE-GLKRQLLKKQTQLSSLNVFVIGAIAKAIATTVTYPMQTVQSILRFGGHRLNPEN
          I.FM..E..LK.QLLKKQ.QLSSLNVFV.GAI.KAIAT.V.Y.MQTVQ.ILRFG.HRL..EN
Retrocopy IRFMS*E<MLKGQLLKKQAQLSSLNVFVTGAIGKAIATRVIYLMQTVQYILRFGCHRLKSEN

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_1808 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1808 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004636	1 retrocopy	retro_cjac_2451,
Macaca mulatta	ENSMMUG00000008106	1 retrocopy	retro_mmul_453,
Monodelphis domestica	ENSMODG00000005569	1 retrocopy	retro_mdom_74,
Monodelphis domestica	ENSMODG00000013036	1 retrocopy	retro_mdom_1808 ,