RetrogeneDB ID: retro_mdom_164

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:38651164..38652151(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025275
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005339
• Aliases: None
• Description: None

Sequence

>retro_mdom_164
ATGGCGAGCTGGAGGGACGATGGCCCTTCGGCCTACATGTTCGAGATGCAGAAGAGGTTCCGTGACCACAACAAGACCAA
AGAGTACCAGGAGCACACTGCCGCAGTGCTCTCAGTGGCCTGGAGCTGTAATGGGGCCCGCCTGGCATCGGGCTCCCTCG
ATAAGACAGCCGGAGTCTTCCTCCTAAAAGATAACGGCCTAGTGAAGGAGTCCAGCTACCAAGGGCACACGGACAGCATC
GACCAGCTGTGCTGGCACCCCAGCAACCCCGATCTCTTCGTCACCGCATCCGGGGACAGGAGTGTTCGCATTTGGGATGT
TCGTCACAACAGGTGTGCCAGCAACATCAAAACCAAAGGTGAGAACATGAATATCTGTTGGAGCCCCGATGGCCTCACTA
TTGCTGTGGGCAATCGAAATGATGTCATTACGTTCATCGATGCCCGCACTCATCGTGTGAAGGCCGAGGAACACTTTAAG
TATGAGGTTAATGAGATCTCCTGGAATAACGAGAATAATCTCTTTTTCCTGACCAATGGGAACGGCTTCATCACTATTCT
CAGTTACCCAGAACTAAAGCCGGTGCAGTCGCTTAATGCCCATCCCTCTAACTGCATCTGTATCAAATTTGATCCAACCG
GCACATATTTTGCCACAGGAAGTGCTGATTCCCTCGTGAGTCTCTGGGATCTCAATGAGATGGTGTGTGTGAGGTGTCTC
TCCAGGCTCGATTGGCCTGTGAGAACCCTCAGTTTCAGCCACGATGGGAAGATGATTGCGTCTGCGTCTGAGGATCATTT
CATCGATATTGCCGAGGTGGAGACAGGAAACAAGGTGTGGGATATACAGTGTGAGTCCCCAACCTTCACCGTGGCCTGGC
ACCCCAAATTTCCACTGCTAGCCTTTGCCTGTGACGACAAAGTCGGTGAGCCTGGGGAATGCCGGGAAACTGGAATTGTG
AAACTGTTTGGCCTTCCTAATGACTCC

Alignment

ORF - retro_mdom_164 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.33 %
• Parental protein coverage: 91.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPSRYVAGMQELFRSHSKTREFPAHSAKVHSVAWSCDGRRLASGSFDKTASVFLLEKDRLVKENNYRGHG
          GPS.Y...MQ..FR.H.KT.E...H.A.V.SVAWSC.G.RLASGS.DKTA.VFLL....LVKE..Y.GH.
Retrocopy GPSAYMFEMQKRFRDHNKTKEYQEHTAAVLSVAWSCNGARLASGSLDKTAGVFLLKDNGLVKESSYQGHT

Parental  DSVDQLCWHPSNPDLFVTASGDKTIRIWDVRTTKCIASVNTKGENINICWSPDGQTIAVGNKDDVVTFID
          DS.DQLCWHPSNPDLFVTASGD...RIWDVR...C.....TKGEN.NICWSPDG.TIAVGN..DV.TFID
Retrocopy DSIDQLCWHPSNPDLFVTASGDRSVRIWDVRHNRCASNIKTKGENMNICWSPDGLTIAVGNRNDVITFID

Parental  AKTHRSKAEEQFKFEVNEISWNNDNNMFFLTNGNGCINILSYPELKPVQSINAHPSNCICIKFDPTGKYF
          A.THR.KAEE.FK.EVNEISWNN.NN.FFLTNGNG.I.ILSYPELKPVQS.NAHPSNCICIKFDPTG.YF
Retrocopy ARTHRVKAEEHFKYEVNEISWNNENNLFFLTNGNGFITILSYPELKPVQSLNAHPSNCICIKFDPTGTYF

Parental  ATGSADALVSLWDVDELVCVRCFSRLDWPVRTLSFSHDGKMLASASEDHFIDIAEVETGDKLWEVQCESP
          ATGSAD.LVSLWD..E.VCVRC.SRLDWPVRTLSFSHDGKM.ASASEDHFIDIAEVETG.K.W..QCESP
Retrocopy ATGSADSLVSLWDLNEMVCVRCLSRLDWPVRTLSFSHDGKMIASASEDHFIDIAEVETGNKVWDIQCESP

Parental  TFTVAWHPKRPLLAFACDDKDGKYDSSREAGTVKLFGLPNDS
          TFTVAWHPK.PLLAFACDDK.G.....RE.G.VKLFGLPNDS
Retrocopy TFTVAWHPKFPLLAFACDDKVGEPGECRETGIVKLFGLPNDS

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	66.39 RPM
SRP007412_cerebellum	0.00 RPM	68.23 RPM
SRP007412_heart	0.00 RPM	67.18 RPM
SRP007412_kidney	0.00 RPM	84.28 RPM
SRP007412_liver	0.00 RPM	84.59 RPM
SRP007412_testis	0.00 RPM	257.92 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_164 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_164 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006495	2 retrocopies	retro_cjac_1571, retro_cjac_3072,
Macropus eugenii	ENSMEUG00000001068	2 retrocopies	retro_meug_1061, retro_meug_19,
Monodelphis domestica	ENSMODG00000005339	1 retrocopy	retro_mdom_164 ,
Mus musculus	ENSMUSG00000025872	2 retrocopies	retro_mmus_1821, retro_mmus_441,
Otolemur garnettii	ENSOGAG00000003503	1 retrocopy	retro_ogar_3005,
Sarcophilus harrisii	ENSSHAG00000010757	1 retrocopy	retro_shar_4,