RetrogeneDB ID: retro_mdom_230

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:493272433..493274284(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000012015
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000016684
• Aliases: None
• Description: None

Sequence

>retro_mdom_230
GCAACATTGATTCCTACAGGTTTGGCACCCCATGTGCCTAAACTACCTCAGAATCCTACAAATATTCAAAAAATCCAAGT
GCCTCCTGGTATGGTCCACATTCTAACGGAGAAGGGACGATTGGCTCTGATTCCTCAACAATCTATGGCACAGGCCCATC
CTGAGGGGCAGAACCAAAATACCATGACTCCTGTTCAGATGTCAACTGTGCAGGCTCCTGGGATAACAACGATTGAGCAA
CAAATGACATCAACTACCATCATGAAGCAAGTGTCTCAGGCGCAGACAGTGGTACAGCCAAGTATAACTTTAGGGCATTC
TCCAACAGTGCAGCCTCAGATTGTTCTGGTTGGTAATGCACAGACAGCAAAGTTACCAATAGCCTCTTCCACATGTTCTG
CACCTTCTCAGATGACTGTACTAGAAGCCACAGCAACTTCTGCTGCTCCAGAAACCGTGGAAAGTGTGAAGAGATGCAAG
AATTTCCTCTCAACACTAATCATGCTGGTTTCATCTTATAAATACGCTCCAAAGATAGCAGCAAATATCAAAGAATTAAT
ACAGAACTGTCTAGAAGGGAAAATTGAAGCTGAAGATTTTGCCAGCAGAACATTTCAAGAATTTCATTCTTCCCCTCCAC
CTTACCTTGCACCTTTCCTGAAGAGGAATTTAGCTGCCCTTCGACAGTCAGTCCCAGATCCCGCAGCTTTCATTCGGCAA
TGTCAGCAGGAACAGCCCAGTGTCCCAGCAACAAGTACCCTGAAAACAGTGGTACTCAAGAGCTCTGGTCAGTGCACAGC
TGGGAAAACTGCTGCCACCTCCTCAAGTACTCGTCAGACACAGTTGACACCAGGCAACGTTAGCAAAGGACAACTTTTAG
CTCTTGTAATCCAACAACCAAAGAAACCAGGGGCACCTCAGCAGGTAACACTGACACCAACCTCTGTGGCGGTGTTGCAA
CAGCCAGACAATCGCATCAGGCTTGTTCCTTCTCAGCAAATTCAACTAAAGCAGCTTCAAACAGCTTCTGTGGTCAAACC
TGCTCTATTACCTGGAACCAAAGTTCTTAATATGACTTTTGCACCAAAGAGTGAAGTGAAAGAACCTGGCCCTTTCAGGG
AGGGTGATGCCATCACTGTTGCATCAACGGCAAGTGTCAACTTATCACAGGAGAGTGCCAGGACATTGACAACAAATTCT
GAATCTGAAGGCACATTAGCAAGTTCTCGTAAAGAGGATACCTTTCTTCTGTCGGGACTTTTACAAAGAAGAATGTTAGA
AATTGGTCAAAAGCATGGAATAACAGAACTGCATCCTGATGTAGTCAGTTATGTGTCACATGCAACAAAGCAAAGGTTAC
GAAACCTCATCGAAAAAGTATCCGAAATTGCTCAACTAAACAATATTTCTTATAAGAATGATAAAAGATATGAACAGACA
AGTAATGTCCAGGCTCAACTCAAATTCTTTAAACAGCTGGACCAAATTGAAAAACAGAGGAAAGATGCACGAGAGAGAGA
ATTTTTAAGGAGTGTGGCAAAGTCTCGATCTAGACAAGAAGATCCAGAACAAGTTAGGTTGAAACAGAGGGCAAAGGAGA
TGCAGCTACAAGAGCTAGAAGAGAGGTGTCAAAGGGATACCAATTTAACTGCATTAGCAGCAATTGGTCCTAGGAAGAAA
AGGAAAGTAGATTCTCTGGGACCTGGATCAGAGACAAAGGGTTCTGGAGATGGAACAACCGAATGGTTTACTCAACAAAG
GAAAACTCGGGTTAAACTCAGGGATCTCATATATTGTTTAGGAAAAGACCAAGTGACAAGGCATTCACTATTATTATACA
AAGCATTCCTT

Alignment

ORF - retro_mdom_230 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.61 %
• Parental protein coverage: 51.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGQLLMLPQQTLAQMQAQAHVQTQPQNTMA---PRPATPTSAPPVQISTVQAPGTPIIARQVTPTTIIKQ
          N.Q....P................PQ..MA...P.........PVQ.STVQAPG...I..Q.T.TTI.KQ
Retrocopy NIQKIQVPPGMVHILTEKGRLALIPQQSMAQAHPEGQNQNTMTPVQMSTVQAPGITTIEQQMTSTTIMKQ

Parental  VSQAQTTVQPTTTLQRSPVVQPQIVLGGTTQTAALGTASAVQPGTPQRTVQGATATSAAATETMENVKKC
          VSQAQT.VQP..TL..SP.VQPQIVL.G..QTA.L..AS.......Q.TV..ATATSAA..ET.E.VK.C
Retrocopy VSQAQTVVQPSITLGHSPTVQPQIVLVGNAQTAKLPIASSTCSAPSQMTVLEATATSAAP-ETVESVKRC

Parental  KNFLSTLIKLASSGKQSTETAANVKELVQNLLDGKIEAEDFTSRLYRELNSSPQPYLVPFLKRSLPALRQ
          KNFLSTLI.L.SS.K.....AAN.KEL.QN.L.GKIEAEDF.SR...E..SSP.PYL.PFLKR.L.ALRQ
Retrocopy KNFLSTLIMLVSSYKYAPKIAANIKELIQNCLEGKIEAEDFASRTFQEFHSSPPPYLAPFLKRNLAALRQ

Parental  LTPDSAAFIQQSQQQQPTTQATTALTAVVLSSSVQRTAGKTAATVTSTLQPPVISLTQPTPVSVSKQGQP
          ..PD.AAFI.Q..QQ.......T......L...V....G...A..T..........TQ.TP..VSK.GQ.
Retrocopy SVPDPAAFIRQC-QQEQPSVPATS----TLKTVVLKSSGQCTAGKTAATSSSTRQ-TQLTPGNVSK-GQL

Parental  TPLVIQQPQKPGALIRSPQVTLTQTPMVALRQPHNRIMLTTPQQIQLNQLQTVPVVKPAVLPGAKALSTV
          ..LVIQQP.KPGA.....QVTLT.T....L.QP.NRI.L..P.Q....Q.Q........V...A....T.
Retrocopy LALVIQQPKKPGA---PQQVTLTPTSVAVLQQPDNRIRLV-PSQ----QIQLKQLQTASVVKPALLPGTK

Parental  SAQAAAAQKNKLKEPGGGSFRDDDDINDVASMAGVNLSEESARILATNSELVGTLTRSCKDETFLLSAPL
          ......A.K...KEPG...FR..D.I..VAS.A.VNLS.ESAR.L.TNSE..GTL..S.K..TFLLS..L
Retrocopy VLNMTFAPKSEVKEPG--PFREGDAIT-VASTASVNLSQESARTLTTNSESEGTLASSRKEDTFLLSGLL

Parental  QRRILEIGKKHGITELHPDVVSYVSHATQQRLQNLVEKVSETAQQKNLSYKDDERYEQASDVRAQLKFFE
          QRR.LEIG.KHGITELHPDVVSYVSHAT.QRL.NL.EKVSE.AQ..N.SYK.D.RYEQ.S.V.AQLKFF.
Retrocopy QRRMLEIGQKHGITELHPDVVSYVSHATKQRLRNLIEKVSEIAQLNNISYKNDKRYEQTSNVQAQLKFFK

Parental  QLDQIEKQRKDEQEREILMRAAKSRSRQEDPEQLRLKQKAKEMQQQELAQMRQRDANLTALAAIGPRKKR
          QLDQIEKQRKD..ERE.L...AKSRSRQEDPEQ.RLKQ.AKEMQ.QEL....QRD.NLTALAAIGPRKKR
Retrocopy QLDQIEKQRKDAREREFLRSVAKSRSRQEDPEQVRLKQRAKEMQLQELEERCQRDTNLTALAAIGPRKKR

Parental  KVDSPGPGSGTEGSGTST
          KVDS.GPGS.T.GSG..T
Retrocopy KVDSLGPGSETKGSGDGT

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	46.49 RPM
SRP007412_cerebellum	0.00 RPM	92.39 RPM
SRP007412_heart	0.00 RPM	31.90 RPM
SRP007412_kidney	0.00 RPM	68.48 RPM
SRP007412_liver	0.00 RPM	36.75 RPM
SRP007412_testis	0.00 RPM	121.20 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_230 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_230 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000010291	4 retrocopies	retro_mluc_2540, retro_mluc_402, retro_mluc_413, retro_mluc_440,
Monodelphis domestica	ENSMODG00000016684	1 retrocopy	retro_mdom_230 ,