RetrogeneDB ID: retro_mdom_1632

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:263187611..263188959(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000009113
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_mdom_1632
ATGCGTGAGTGCATCTCTATCCACGTTAGCCAGGCTGGTGTCCAGATTGGCAATGCCTGCTGGGAGCTGTACTGCCTGGA
ACATGGTATCCAGCCTGATGGGCAGATGCCAAGTGATAAGACCATTGGGGGAAGGAGATGACTCCTTCAACACCTTCTTC
AGCAAAACAGGGGCTGGCAAGCATGTCCCCAGAGCAGTGTTTGTAGATCTGGAACCAACTGTCATTGATGAAGTTCATAC
TGGAACTTACTGCCAGCTCTTTCATCCTGAGCAGCTGATCACTGGCAAGGAAGATGCTGCCAATAACTATGCCCGTGGAC
ACTACACTATTGGCAAGGAAATCATCGACATGATTCTGGACAGAATTTGGAAGCTTGCGGATCAGTGCACAGGTCTTCAA
GGCTTCTTGGTTTTCCACAGCTTTGGTGGTGGGACTGTCTCTGGTTTCACCTCTCTGCTGATGGAAAGGCTGTCTGTTGA
TTATGGCAAAAAGTCCAAGCTGGAGTTCTCCATTTACCCAGCCCCACAGGTTTCCACTGCTGTGATTGAGCCCTACAACT
CCATTCTGACCACTCACACCACCCTGGAGCACTCTGATTGTGTCTTCATGGTAGACAATGAGGCTATCTATGATATCTGT
CGCAGAAACCTTGATATTGAACACCCAACCTACACTAATCTAAATCGCCTTATTAGTCAAATTGTGTCCTCCATCACTGC
CTCTCTGAGATTTGATGGTGCCCTGAATGTTGATCTGACAGAATTCCAGACCAACTTGGTGCCCTACCCCCAAAAACATT
TCCCCCTGGCCACATATGCCCCAGTCATCTCTGCTGAGAAAGCCTACTATGAGCAGCCAACTGTAGCAGAGATCACCAAT
GCCTGCTTTGAGCCTGCCAACCAGATGGTGAAATGTGACCCTTGCCATGGTAAATACATGGCTTGCTGCCTGCTGTACCG
TGGGGATGTGGTACCCAAAGATGTCAATGCCGCCATTGCCACCATCAAGACAAAGCGAAGCATCCAGTTTGTGGATTGGT
GCCCAACTGGCTTCAAGGTTGGCATCAATTACCAGCCTCCCACTGTGGTTCCTGGTGGTGACCTGGCCAGGGTACAGAGG
ACTGTGTGCATGCTGAGCAACACTACAGCCATTGCTAAGGCCTGGGCTCTCCTGGACCACAAGTTTGATCTGATGTATGC
CAAACGTGCCTTTGTTAACTGGTATGTGGGGGAGGGCATAGAGGAAGGAGAGTTCTCTGAGGCACGGGAGGATATGGCAG
CCTTGGAGAAGGATTATGAGGAGGTTGGAGCAGATAGTGCAGACAGGGAAGATGAAGGTGAGGAATAT

Alignment

ORF - retro_mdom_1632 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGG-GDDSFNTFFSETGAGKHVPRAVFVD
          MRECISIHV.QAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGG.GDDSFNTFFS.TGAGKHVPRAVFVD
Retrocopy MRECISIHVSQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGG>GDDSFNTFFSKTGAGKHVPRAVFVD

Parental  LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFH
          LEPTVIDEV.TGTY.QLFHPEQLITGKEDAANNYARGHYTIGKEIID..LDRI.KLADQCTGLQGFLVFH
Retrocopy LEPTVIDEVHTGTYCQLFHPEQLITGKEDAANNYARGHYTIGKEIIDMILDRIWKLADQCTGLQGFLVFH

Parental  SFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAI
          SFGGGT.SGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAV.EPYNSILTTHTTLEHSDC.FMVDNEAI
Retrocopy SFGGGTVSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVIEPYNSILTTHTTLEHSDCVFMVDNEAI

Parental  YDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAE
          YDICRRNLDIE.PTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYP..HFPLATYAPVISAE
Retrocopy YDICRRNLDIEHPTYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPQKHFPLATYAPVISAE

Parental  KAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPT
          KAY.EQ..VAEITNACFEPANQMVKCDP.HGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPT
Retrocopy KAYYEQPTVAEITNACFEPANQMVKCDPCHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPT

Parental  GFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFS
          GFKVGINYQPPTVVPGGDLA.VQR.VCMLSNTTAIA.AWA.LDHKFDLMYAKRAFV.WYVGEG.EEGEFS
Retrocopy GFKVGINYQPPTVVPGGDLARVQRTVCMLSNTTAIAKAWALLDHKFDLMYAKRAFVNWYVGEGIEEGEFS

Parental  EAREDMAALEKDYEEVGVDSVEGEGEEEGEEY
          EAREDMAALEKDYEEVG.DS.....E.EGEEY
Retrocopy EAREDMAALEKDYEEVGADS--ADREDEGEEY

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_1632 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1632 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,