RetrogeneDB ID: retro_mdom_348

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:251078863..251079816(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1B
• Ensembl ID: ENSMODG00000015206
• Aliases: None
• Description: tubulin, alpha 1b [Source:HGNC Symbol;Acc:18809]

Sequence

>retro_mdom_348
ATGCGTGAGTGCATCTCTATCCACGTTGGCCAGGCTGATGTCCAGATTGCCAATGCCTGCTGGGAGCTGTACTGCTTGGA
ACATGGTATCTAGCCTGATGGGCAGATGCCAAGTGACAAGACCATTGTAGGAGGAGATGACTCCTTCAACACCTTCTTCA
GCAAAATGGGGGCTGGCAAGCATGTCCACAGAGCAATGTTTGTAGATCTGGAACCAACTGTCATTGATGAAGTTCGTACT
GGAACTTACCGCCAGCTCTTCCATCCTGAGCAGCTGATCACTGGCAAGGAAGATGCCGCCAATAACTACGCCCGTGGACA
CTGCACTATTGGCAAGGAAATCATCAACATGGTTCTGGACAGAATTCGGAAGCTTATGGATCAGTGCATGGGTCTTCAAG
GCTTCTTGGTTTTCCACAGCTTTGGTGGTGGGACTGGCTCTGGTTTCACCTCTCTGCTGATGGAAAGGCTGTCTGTTGAT
TATGGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCACAGGTTTCCACCACTGTGGTTGAGCACTACAACTC
CATTCTGACCACTCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCTATCTATGATATCTGTC
ACAGAAACCTTGATATCGAACACCCAACCTACACTAATCTAAATCGCCTTATTAATCAAATTGTGTCCTCCATCACTGCC
TCTCTGAGATTTGATGGTGCCCTGAATGTTGATCTGACAAATTCCAGACCAACTTGGTGCTCTACCCCCGAATCTATTTC
CCCCTGGCCACATCCGCCCCAGTCATCTCTGCTGTGAAAGCCTACCATGAGCAGCTGACTGTAGCAGAGATCACCAATGC
TTGCTTTGAGCCTGACAACCAGATGGTGAAATGTGACCCTTGCAACAGTAAATACATGGCTTGCTGTACCATG

Alignment

ORF - retro_mdom_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.28 %
• Parental protein coverage: 70.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGKHVPRAVFVDL
          MRECISIHVGQA.VQI.NACWELYCLEHGI.PDGQMPSDKTI.GGDDSFNTFFS..GAGKHV.RA.FVDL
Retrocopy MRECISIHVGQADVQIANACWELYCLEHGI*PDGQMPSDKTIVGGDDSFNTFFSKMGAGKHVHRAMFVDL

Parental  EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHS
          EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGH.TIGKEII..VLDRIRKL.DQC.GLQGFLVFHS
Retrocopy EPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHCTIGKEIINMVLDRIRKLMDQCMGLQGFLVFHS

Parental  FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIY
          FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVST.VVE.YNSILTTHTTLEHSDCAFMVDNEAIY
Retrocopy FGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTTVVEHYNSILTTHTTLEHSDCAFMVDNEAIY

Parental  DICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLT-EFQTNLVPYPRIHFPLATYAPVISAE
          DIC.RNLDIE.PTYTNLNRLI.QIVSSITASLRFDGALNVDLT..FQTNLV.YPRI.FPLAT.APVISA.
Retrocopy DICHRNLDIEHPTYTNLNRLINQIVSSITASLRFDGALNVDLT<KFQTNLVLYPRIYFPLATSAPVISAV

Parental  KAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLL
          KAYHEQL.VAEITNACFEP.NQMVKCDP...KYMACC..
Retrocopy KAYHEQLTVAEITNACFEPDNQMVKCDPCNSKYMACCTM

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	80.34 RPM	0.00 RPM
SRP007412_cerebellum	157.35 RPM	0.00 RPM
SRP007412_heart	20.33 RPM	0.00 RPM
SRP007412_kidney	106.66 RPM	0.00 RPM
SRP007412_liver	19.64 RPM	0.00 RPM
SRP007412_testis	23.18 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_348 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_348 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 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012244	1 retrocopy	retro_btau_402,
Choloepus hoffmanni	ENSCHOG00000008444	2 retrocopies	retro_chof_179, retro_chof_360,
Callithrix jacchus	ENSCJAG00000020874	2 retrocopies	retro_cjac_1603, retro_cjac_1861,
Felis catus	ENSFCAG00000028689	3 retrocopies	retro_fcat_1802, retro_fcat_254, retro_fcat_798,
Homo sapiens	ENSG00000123416	1 retrocopy	retro_hsap_808,
Macropus eugenii	ENSMEUG00000010779	2 retrocopies	retro_meug_1648, retro_meug_2174,
Macropus eugenii	ENSMEUG00000011167	4 retrocopies	retro_meug_1121, retro_meug_157, retro_meug_1616, retro_meug_1964,
Monodelphis domestica	ENSMODG00000015206	2 retrocopies	retro_mdom_1632, retro_mdom_348 ,
Monodelphis domestica	ENSMODG00000023336	1 retrocopy	retro_mdom_973,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607, retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Otolemur garnettii	ENSOGAG00000009435	1 retrocopy	retro_ogar_240,
Pan troglodytes	ENSPTRG00000012950	1 retrocopy	retro_ptro_2158,
Sus scrofa	ENSSSCG00000000190	2 retrocopies	retro_sscr_380, retro_sscr_702,