RetrogeneDB ID: retro_mdom_2013

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:32230215..32231436(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MITF
• Ensembl ID: ENSMODG00000003754
• Aliases: None
• Description: microphthalmia-associated transcription factor [Source:HGNC Symbol;Acc:7105]

Sequence

>retro_mdom_2013
ATGCCAGCATGTCAGGTTCAGACCCATCTAGAAAATCCCACCAAGTACCACATTCAGCAAGCCCAAAGGCAACAGGTAAA
GCAGTACTTTTCTACCACTTTAGCCAATAAACATGCCAACCAAGCCCGGAGCTTGCCTTGTCCAAACCAGCCTGGGGACC
ATGTCATGCCACCTGGACCTGGGAGCAGTACACCAAATAGCCCCATGGCTATGCTCACACTTAACTCCAACTGTGAAAAA
GAGGAGTTTTATAAGTTTGAAGAGTAGAACAGGGCTGAGAGTGAGTACCCAAATATGAACGCGCATTCTCAAGCATCATG
CATGCAGATAGATGATGTAATTGATGACATAATTAGCCTCGAGTCAAGCCCTAATGAAGAAATCCTAGGCCTGATGGATC
CAGCATTGCATATGGTCAATACATTACCTGTTTCTGGAAATTTGATTGACCTTTATGGCAACCAAGGCATGCCACCTCCA
GGGCTGGAAACCAGCAACTCCTGTCCAGTCAATCTTCCCAATATTAAAAGGGAACTCACTGCATGTATTTTCCCTACAGA
ATCAGAAGCAAGGGCATTGGCCAAAGAGAGACATAAAAAGGACAATCACAATTTAATTGAAGGGCGGAGGAGATTTAATA
TCAATCACCTCATTAAAGAGCTAGGCACTTTGATACTAAAGTCAAATGACCCAAATATGCATTGGAAAAAGGGAACTATT
TTGAAAGCAACTGTGGATTACATCTGAAAACTGCAGCAAGAACAGCAGTGGGCAAAAGAACTTGAAAATGGACAGAAGAA
ACTGGAACACTCTAACAGGCATCTTTTGCTCAGAATACAGGAACTTGAGGTACAGGCTTGAGTACATGGACTTTCCCTCA
TTCCATCTACAGGACTTTGCTCCCCAGAACTGGTGAACTGTGTCATCAAACAAGAACCAATTCTTGAAAACTGCAGTCAG
GATGTCCTTCAGCATCACTCAGACCTCGCCTGCATGACCACCCTTGATCTTACAGATGGCACCATCACTTTCAGTAATAA
TTTGGGGAATGGTATTGAAACACCAGCCTACAGCGTTCCTACAAAAATGGGCTCCAAACTGGAAGACATCTTGATGGATG
ATACTCTCTCCCCCAATCCACTTCTCTTATTGGTATCCCCTGGAGCTTCCAAAGCAAGTAGCCGGAGGAGCAGCATGATG
GAAGATACTGATCATGCCTGT

Alignment

ORF - retro_mdom_2013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.65 %
• Parental protein coverage: 78.52 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVLKVQTHLENPTKYHIQQAQRQQVKQYLSTTLANKHANQALSLPCPNQPGDHVMPPGPGSSAPNSPMA
          M....VQTHLENPTKYHIQQAQRQQVKQY.STTLANKHANQA.SLPCPNQPGDHVMPPGPGSS.PNSPMA
Retrocopy MPACQVQTHLENPTKYHIQQAQRQQVKQYFSTTLANKHANQARSLPCPNQPGDHVMPPGPGSSTPNSPMA

Parental  MLTLNSNCEKEGFYKFEEQNRAESECPNMNTHSRASCMQMDDVIDDIISLESSYNEEILGLMDPALQMAN
          MLTLNSNCEKE.FYKFEE.NRAESE.PNMN.HS.ASCMQ.DDVIDDIISLESS.NEEILGLMDPAL.M.N
Retrocopy MLTLNSNCEKEEFYKFEE*NRAESEYPNMNAHSQASCMQIDDVIDDIISLESSPNEEILGLMDPALHMVN

Parental  TLPVSGNLIDLYGNQGMPPPGLAISNSCPANLPNIKRELTACIFPTESEARALAKERQKKDNHNLIERRR
          TLPVSGNLIDLYGNQGMPPPGL..SNSCP.NLPNIKRELTACIFPTESEARALAKER.KKDNHNLIE.RR
Retrocopy TLPVSGNLIDLYGNQGMPPPGLETSNSCPVNLPNIKRELTACIFPTESEARALAKERHKKDNHNLIEGRR

Parental  RFNINDRIKELGTLIPKSNDPDMRWNKGTILKASVDYIRKLQREQQRAKELENRQKKLEHANRHLLLRIQ
          RFNIN..IKELGTLI.KSNDP.M.W.KGTILKA.VDYI.KLQ.EQQ.AKELEN.QKKLEH.NRHLLLRIQ
Retrocopy RFNINHLIKELGTLILKSNDPNMHWKKGTILKATVDYI*KLQQEQQWAKELENGQKKLEHSNRHLLLRIQ

Parental  ELEMQARAHGLSLIPSTGLCSPELVNRVIKQEPILENCSQDVLQHHPDLTCTTTLDLTDGTITFSNNLGN
          ELE.QA..HGLSLIPSTGLCSPELVN.VIKQEPILENCSQDVLQHH.DL.C.TTLDLTDGTITFSNNLGN
Retrocopy ELEVQA*VHGLSLIPSTGLCSPELVNCVIKQEPILENCSQDVLQHHSDLACMTTLDLTDGTITFSNNLGN

Parental  GTETTTAYSVPTKMGSKLEDILMDDTLSPVGVTDPLLSSVSPGASKASSRRSSMSMEDTDHAC
          G.E.T.AYSVPTKMGSKLEDILMDDTLSP.....PLL..VSPGASKASSRRSSM.MEDTDHAC
Retrocopy GIE-TPAYSVPTKMGSKLEDILMDDTLSP----NPLLLLVSPGASKASSRRSSM-MEDTDHAC

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_2013 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2013 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000003754	1 retrocopy	retro_mdom_2013 ,