RetrogeneDB ID: retro_mdom_4

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:256169125..256170130(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024783
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011967
• Aliases: None
• Description: None

Sequence

>retro_mdom_4
ATGTTTCTGGCGGTGCTGACCTCTGTACGCCTCAGAGGGGCCGTGGCTTTATTACTAAGATTTCGGAGTACCCTAGTAAT
AGTTGAGCATGAGAATGATGCACCAGCATCCATTACATTAAATACAGTGACTGCAGCCACACAGCTTGGTGGAGGAGTAT
CTTGTTTAGTAGCTGGAACCAAATGTGATGTAGTGGCCCGGGATCTGTGTAAGGTGAAGGGTGTAACCAAGGTCCTGGTG
GCTCAGCATGACATGTTCAAAGGACTCCTTCCAGAGGAACTGACACCTTTAATTCTGGCAACACATCGGCAGTACAATTA
CACACACATCTGTGCTGGAGCATCATCCTTTGGGGAGAACTTGTTGCCCAGAGTAGCAGGCAAACTTGATGTTTCTCAGA
TTTCTGACATCATTCAAATCAAGTCGCCAGATACTTTTGTAAGAACTCTTTATGCAGGAAAGATTATATGTACTGTTAAG
TGTGAGGAGAAAGTCAAGGTGTTCTCTGTTCAAGGTACTGCGTTTGAGACAGCGGCCACAAGTGGGGGAAATGCCAGTGT
AGAGAATGCACCCACTATCTCCCCAGTGGGGTTGTCTGAATGGCTTCACCAGACATTACTAAAAAATGATTGGCCACATC
TGACTAGTGCCAAGTCGGTGGTATGTGGAGGACTTGGTTTGAAGACTAGGGAGAATTTTAAGCTATTATATGACTTGGCA
GAACAGCTGCGTGCTTCAGTTAGTGCTACCCTTGCTGCTGTTAATGCAGGCTTTGTGCCCAAAGACCTGTTAGTTGGAGA
GAGAGGAAAAAACAAAACACCGAAGCTATATGTTGCTGTGGGCATATCCGGGTTCATGCAACATTTGGCAGAAATAAAAG
ACAGCAAGACCATTGTAGCCATCAATGAGGATCCGGAAGCCCCAATTTTCCAGGTGGCAGACCTTGGAATAGTTGCAGAT
TTATTTAAGGTGGTCCCTGAGTTGACTGAGCTATTAAAGAAGAAA

Alignment

ORF - retro_mdom_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.91 %
• Parental protein coverage: 97.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLRRATASLLRCQSTLVIAEHANDALASITLNTVTAATRLGGEVSCLVAGTKCDKVAQDLCKVTGVAKVL
          RLR.A.A.LLR..STLVI.EH.NDA.ASITLNTVTAAT.LGG.VSCLVAGTKCD.VA.DLCKV.GV.KVL
Retrocopy RLRGAVALLLRFRSTLVIVEHENDAPASITLNTVTAATQLGGGVSCLVAGTKCDVVARDLCKVKGVTKVL

Parental  VAQHDAFKGLLPEELTPLILAAQKQFNYTHICAGASAFGKNLLPRVAAKLDVAPISDIIQIKSPDTFVRT
          VAQHD.FKGLLPEELTPLILA...Q.NYTHICAGAS.FG.NLLPRVA.KLDV..ISDIIQIKSPDTFVRT
Retrocopy VAQHDMFKGLLPEELTPLILATHRQYNYTHICAGASSFGENLLPRVAGKLDVSQISDIIQIKSPDTFVRT

Parental  IYAGNAICTVKCEEKVKVFSVRGTAFEAATTSGGSASTEKAPSTSPVGLSEWLDQKLTKSDRPELTSAKV
          .YAG..ICTVKCEEKVKVFSV.GTAFE.A.TSGG.AS.E.AP..SPVGLSEWL.Q.L.K.D.P.LTSAK.
Retrocopy LYAGKIICTVKCEEKVKVFSVQGTAFETAATSGGNASVENAPTISPVGLSEWLHQTLLKNDWPHLTSAKS

Parental  VISGGRGLKSGENFKLLYDLADQLHAAVGASRAAVDAGFVSNDLQVGQTGKIVAPSLYIAVGISGAIQHL
          V..GG.GLK..ENFKLLYDLA.QL.A.V.A..AAV.AGFV..DL.VG..GK...P.LY.AVGISG..QHL
Retrocopy VVCGGLGLKTRENFKLLYDLAEQLRASVSATLAAVNAGFVPKDLLVGERGKNKTPKLYVAVGISGFMQHL

Parental  AGMKDSKSIVAINKDPEAPIFQVADFGIVADLFKVVPEMTELLKKK
          A..KDSK.IVAIN.DPEAPIFQVAD.GIVADLFKVVPE.TELLKKK
Retrocopy AEIKDSKTIVAINEDPEAPIFQVADLGIVADLFKVVPELTELLKKK

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	160.20 RPM
SRP007412_cerebellum	0.00 RPM	252.02 RPM
SRP007412_heart	0.00 RPM	3114.87 RPM
SRP007412_kidney	0.00 RPM	1212.80 RPM
SRP007412_liver	0.00 RPM	1472.71 RPM
SRP007412_testis	0.00 RPM	125.72 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_4 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_4 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011967	1 retrocopy	retro_mdom_4 ,
Ochotona princeps	ENSOPRG00000000755	1 retrocopy	retro_opri_1148,
Xenopus tropicalis	ENSXETG00000015322	1 retrocopy	retro_xtro_65,