RetrogeneDB ID: retro_mdom_1336

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:58346127..58347503(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000020916
• Aliases: None
• Description: None

Sequence

>retro_mdom_1336
GCCAAATGTTTTAACAGAAGAGCATACTGTGGCCAGTGCAGTGAATGGATATGGGGTCTCAGAAGGCAAGACTACAAGTA
TAACAACTGCAAATTACTGGTCCATAAACGTTGTCATATACTTGTACCACTGACCTGCAAAAGGCATATGGATTCAGTGA
TGCCTTCCCAAGAACATGAAATAGATGATAAAAATGATGAAGTTGACCTTCCCTCCAACAAAAATGATGGACTCACTTAT
ATTCCCTCAACCCGGAAGCATGACAGCCTTAAAGATGATTCTGAGGACATTAAGCCAGTTATTGATGGGATGGATGGAAT
TAAAATATCGCAGGGGCTTGGGCTGCAGGACTTCGATTTAATCAGAGTTATTGGACAGGGGAGTTATGCCAAAGTTCTCT
TAGTGCGATTGAAAAAAAATGACCATATTTATGCCATGAAGGTAGTCAAAAAAAGGTAGTGGTCCACGATGACGAACACA
TCGACTGGGTGCAGACAGAGAAGCATGTATTTTAACAGGCCCCCAGAAACCCATTCCTTGTTGGCCGGCACTCCTGCTTC
CAAACAACAAGTCAGTCATTCCTTGTCATCGAGTATGTGAATGGAGGAGATTTCATGTTTTATATGCAAAGGTAAAGAAA
GCTTCCGGAGGATCACTTCAGGTTTTATGCTGCTGAAATATGTATTGCTCTAAACTTTCTCCATGAATGAGGAATTATCT
ACAGGGACTTAAAACTAGATAATGTGCTCCTAGATTCCAAAGGTCACATCAAATTAACAGATTATACCATGTGAAAGGAA
GGTTTGAGCCAAGGTGACACAACAAGCACTTTCTGTGGGACACCAAATTATATTGCACCCAAAATCCTAAGGGGAGAAGA
ATTCGAGTTCAGTGCAGAATGGTGGGCTCTTGCTGTCTTGATATTTGAGATGATGGCAGGAAGAGCATCATTTGATATAA
TCACAGACAATCTGGACATGAACACTGAAGATTAACTCTTCCAAGTTAATCTTGAGAAGCCTATTTGAATCCCCAGATTT
CTCTCTGTCAAAGCTTACCACATCTTAAAAAGATTTTTAAATAAGGATCCCAAAGAGAGGCTTGGTTGCCAATCACAAAT
GGGATTTTCAGATATCAAGTCTCATACGTTCTTCTGCAGCATAGACTGGGATCTACTGGAGAATAAGCAAGCCCTCCCTC
CATTTCAGCCTCAGACAACCAATGATTATGATCTGGAAAACTTCGATACACAGTACACCAGTGAACCTGTGCAGCTAACC
CCAGATGACGAGGATGTAATCAAAAGAATAGACCAGTCAGGATTTGAAGGATTTGAATACATCAATCCCTTGTTGCTTTC
TACAGAAGAGTCGGTA

Alignment

ORF - retro_mdom_1336 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.43 %
• Parental protein coverage: 80.35 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKRFNRRAYCGQCSERIWGLGRQGYKCINCKLLVHKRCHILVPLTCKRHMDSVMPSQEPQIDDKNDEVDL
          AK.FNRRAYCGQCSE.IWGL.RQ.YK..NCKLLVHKRCHILVPLTCKRHMDSVMPSQE..IDDKNDEVDL
Retrocopy AKCFNRRAYCGQCSEWIWGLRRQDYKYNNCKLLVHKRCHILVPLTCKRHMDSVMPSQEHEIDDKNDEVDL

Parental  PSEENDGLAYIPSTRKHDSLKDDSEDIKPVIDGMDGIKISQGLGLQDFDLIRVIGRGSYAKVLLVRLKKN
          PS..NDGL.YIPSTRKHDSLKDDSEDIKPVIDGMDGIKISQGLGLQDFDLIRVIG.GSYAKVLLVRL...
Retrocopy PSNKNDGLTYIPSTRKHDSLKDDSEDIKPVIDGMDGIKISQGLGLQDFDLIRVIGQGSYAKVLLVRLXXX

Parental  DQIYAMKVVK-KELVHDD-EDIDWVQTEKHVFEQASSNPFLVGLHSCFQTTSRLFLVIEYVNGGDLMFHM
          D.IYAMKVVK.K..V..D.E.IDWVQTEKHVF.QA..NPFLVG.HSCFQTTS..FLVIEYVNGGD.MF.M
Retrocopy DHIYAMKVVK<KKVVVHDDEHIDWVQTEKHVF*QAPRNPFLVGRHSCFQTTSQSFLVIEYVNGGDFMFYM

Parental  QRQRKLPEEHARFYAAEICIALNFLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLGPGDTTSTFC
          QR.RKLPE.H.RFYAAEICIALNFLHE.GIIYRDLKLDNVLLDS.GHIKLTDY.M.KEGL..GDTTSTFC
Retrocopy QR*RKLPEDHFRFYAAEICIALNFLHE*GIIYRDLKLDNVLLDSKGHIKLTDYTM*KEGLSQGDTTSTFC

Parental  GTPNYIAPEILRGEEYGFSVDWWALGVLMFEMMAGRSPFDIITDNPDMNTEDYLFQVILEKPIRIPRFLS
          GTPNYIAP.ILRGEE..FS..WWAL.VL.FEMMAGR..FDIITDN.DMNTED.LFQV.LEKPI.IPRFLS
Retrocopy GTPNYIAPKILRGEEFEFSAEWWALAVLIFEMMAGRASFDIITDNLDMNTED*LFQVNLEKPI*IPRFLS

Parental  VKASHVLKGFLNKDPKERLGCQPQTGFSDIMSHTFFRSIDWDLLEKKQALPPFQPQITDDYGLDNFDTQF
          VKA.H.LK.FLNKDPKERLGCQ.Q.GFSDI.SHTFF.SIDWDLLE.KQALPPFQPQ.T.DY.L.NFDTQ.
Retrocopy VKAYHILKRFLNKDPKERLGCQSQMGFSDIKSHTFFCSIDWDLLENKQALPPFQPQTTNDYDLENFDTQY

Parental  TSEPVQLTPDDEDVIKRIDQSEFEGFEYINPLLLSTEESV
          TSEPVQLTPDDEDVIKRIDQS.FEGFEYINPLLLSTEESV
Retrocopy TSEPVQLTPDDEDVIKRIDQSGFEGFEYINPLLLSTEESV

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_1336 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1336 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000020916	3 retrocopies	retro_mdom_1158, retro_mdom_1336 , retro_mdom_1463,
Mus musculus	ENSMUSG00000029053	1 retrocopy	retro_mmus_3013,