RetrogeneDB ID: retro_mdom_1304

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:352638422..352639672(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013487
• Aliases: None
• Description: None

Sequence

>retro_mdom_1304
GTCGTGAAGATGAGGAAAAAAGTGAAGAGAACTCGAGTTTTGGTTATTTGCAGGCTTACCAGGCATGTCGCCAAACTGAA
GTCAAAAAAGGGTACTGAAGATACATTAGTGAAAAATCAAAGATGAACACAAAGATTACTTGAAGAAATTAATGCTATGA
AGGATGTAAAACCTCATGAAGTAACTAAATCTGCTCTCAATGATGATATCAACTTTGAAAAAATCTGCAAAAAATCCAGA
TTCTACAGCAACTGAAAGAACAATTGCTAGGCTAGCTAAACATCCATTATTGAAGAAGAAAAAAATAGATGCACTAAAAG
CTGCTGTCAGAGCATTTAAAGATGCAAGACAGAATATTACTGAAGGCGATTCATTGAAAGATTCTTCAGAAGAAAATTAC
AGTGAGGAGACAGTGATAAAGCAAAGCTCTCATAACAATTTGAATAAATTCAAACACCAAGAAAGTACAGTAAAAAAGGG
AGGAAATGTTAAAACATCAAAGAAGCCAAACATACTTGAAAAAAATGGGTAAGGTAGAACATGAACAAAAAATGGGGAAC
CCTTCACATGTGGCATTAAAACCTTCTCAAATGTCTTCCCAGATTGATTGTGAAACCCAAAATACACCTGTAGAACCAGA
AAAGAAAAATCTCCCCAGTACTAACAAGGTAAACAGATAAAAAATTTCTACTGTTACTAATAATAATGACAGTGATCTGG
TAGAACAGAGTGAAGAAGAAAAGGAATATTTCGATGATAGCACAGAAGAAAGGTTTTATAAACAGTCTTCACTGTCTGAA
GATAGTGATAGTGATGATGATTTCTTTATTGGTAAAATTAAGCGAACCAGAAAGAAGGAAAATAGTTGATCTTCATTTAA
GGACCAAAAGACTCCCAAAAAATCATTTCCTGAAAAAGAAAAGTTTGAGACTCTGAAGAGTGTGGAATAAATGAGGCCAA
CTACCAAAGCCAGGACACTAGAATCAACATTTTTTTTCTTCTTTATCTGAATCCAGAAGGACAAGAAGAAATGACAGAGA
ACATCCTCCTAAAAACAGAAGTCCAGCATGTCAACAAAATGAAACTCAGATCAAGAATCACCTTGACAGAGGTGTGCATA
CAAAACCTGAAAATAAGAAGTCTCAGTTGCAGCAGCCCCTTCAGCCTTCTTGGGAAGTAAGTTGGAAATGAAAAGAACAA
ATGTCTAAAATTACAGAATTTCAAGGGAAAAAATTACATTTGATGATGAC

Alignment

ORF - retro_mdom_1304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.49 %
• Parental protein coverage: 97.2 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VVKMRKEVKRTRVLVIRRLTRHIAKLKSKKGTEDTLVKNQRRTQRLLEEIHAMKDVKPDEVTKTALDDDI
          VVKMRK.VKRTRVLVI.RLTRH.AKLKSKKGTEDTLVKNQR.TQRLLEEI.AMKDVKP.EVTK.AL.DDI
Retrocopy VVKMRKKVKRTRVLVICRLTRHVAKLKSKKGTEDTLVKNQR*TQRLLEEINAMKDVKPHEVTKSALNDDI

Parental  NFEKICKK-PDSTATERAIARLATHPLLKKK-IDALKAAVRAFKDARHNITEGDSLKDSSEENYSEETGI
          NFEKICKK.PDSTATER.IARLA.HPLLKKK.IDALKAAVRAFKDAR.NITEGDSLKDSSEENYSEET.I
Retrocopy NFEKICKK>PDSTATERTIARLAKHPLLKKKKIDALKAAVRAFKDARQNITEGDSLKDSSEENYSEETVI

Parental  KQSSHNNLNTFKHQESTVKKGEN-VKTSKKPNILEKKMGKVEHEQKMGNPSHVALKPSQKSSQIDCETQN
          KQSSHNNLN.FKHQESTVKKG.N..K.......L.KKMGKVEHEQKMGNPSHVALKPSQ.SSQIDCETQN
Retrocopy KQSSHNNLNKFKHQESTVKKGGN>LKHQRSQTYL-KKMGKVEHEQKMGNPSHVALKPSQMSSQIDCETQN

Parental  TPVEPEKKNLPSANKINRSKCSTVITNNDSDLEEQSEEEKEYFDDSTEERFYKQSSLSEDSDSDDDFFIG
          TPVEPEKKNLPS.NK.NR.K.STV..NNDSDL.EQSEEEKEYFDDSTEERFYKQSSLSEDSDSDDDFFIG
Retrocopy TPVEPEKKNLPSTNKVNR*KISTVTNNNDSDLVEQSEEEKEYFDDSTEERFYKQSSLSEDSDSDDDFFIG

Parental  KIKRTRKKENSCSSSFKDQKTPKKSFPEQEKLETLKSVEKTRPTTKARRLEST-FFSSLSESRRTRRNAR
          KIKRTRKKENS..SSFKDQKTPKKSFPE.EK.ETLKSVE..RPTTKAR.LEST....SLSESRRTRRN.R
Retrocopy KIKRTRKKENS-*SSFKDQKTPKKSFPEKEKFETLKSVE*MRPTTKARTLEST>XXXSLSESRRTRRNDR

Parental  EHPPKNRIPAFQQNETQIKNHVDRGVHAKPENKKPQLQQPLHPSWEASRKRKEQMSKITVFQGK-KITFD
          EHPPKNR.PA.QQNETQIKNH.DRGVH.KPENKK.QLQQPL.PSWE.S.K.KEQMSKIT.FQGK.KITFD
Retrocopy EHPPKNRSPACQQNETQIKNHLDRGVHTKPENKKSQLQQPLQPSWEVSWK*KEQMSKITEFQGK<KITFD

Parental  DD
          DD
Retrocopy DD

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_1304 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1304 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017177	1 retrocopy	retro_cjac_1132,
Monodelphis domestica	ENSMODG00000013487	2 retrocopies	retro_mdom_1304 , retro_mdom_1705,
Otolemur garnettii	ENSOGAG00000032423	1 retrocopy	retro_ogar_1270,
Tarsius syrichta	ENSTSYG00000006869	1 retrocopy	retro_tsyr_1456,