RetrogeneDB ID: retro_mdom_117

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:345379676..345380996(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000023726
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TUBB4B
• Ensembl ID: ENSMODG00000017213
• Aliases: None
• Description: tubulin, beta 4B class IVb [Source:HGNC Symbol;Acc:20771]

Sequence

>retro_mdom_117
ATGAGGGAGATCATGCCCCTCCAGGCCAGGCAATGCCAGATCAGCACAAAGTTCTGGGAGGTGATCAGTGACAAGCATGG
TATTGACCCTACCAGAACTTACCATGGGGAGAGCAACCTGCAGCTGGAGAGGATTCATATCTACTATAATGAAGCAACTG
GTGGGAAATATGTGCCCCGGGCAGTTCTGGTCGATCTTGAGCCTGGAACAATGGACTCCGTCCGGTCTGGACCTTTCGGA
CAGATTTTCAGGCCAGACAACTTTGTCTTCGGCCAGAGTGTTGCTGGAAACAACTGGGCAAAAGGCCACTACACAGAAGG
TGCGGAACTGGTTGACTCAGTATTGGATGTTGTAAGAAAAGAAGCTGAAAGTTGTGACTGTCTCCCGGGATTCCAGCTGA
TGCACTCTCTGGGTGTTGGGACTGGGTCTGGAATGGGTACCCTCTTAATCAGCAAGATCCGGGCAGATAGAATCATGAAC
ACTTTCAGCGTTGTATCCTCCCCCAAGGTATTGGACACTGTAGTAGAACCCTACAATGCAACCCTCTCAGTACACCAGCT
TGTAGAAAACACAGATGAAACCTATTGTATTGATAATGAAGCCTTCTACAATATCTGTTTTAGAACCCTGAAACTGACCT
CTCCCACATATGGTGATCTGAACCACCGGGTGTCAGCAACCATGAGTGGCGTCACCACCTGCTTATGTTTCCCAGGGCAG
CTTAACATTGATTTGAGTAAGCTGGCAGTGAACTTGGTCACCTTTCCCCGTCTGCACTTCTTTATGCCTGGCTTTGCTCC
ACTAACTATCTGTGGTAGCCAGCAGTACCATGCTTTAACCGTGCCAGAGCTTACCCAGCAGATGTTTGATGCAAAGAACA
TGATGGCTGCTTGTGACCCATGGCATGGGTGCTATCTTACAGTAGCAGCTGTGTTCAGAGGCCATATATCCATGAAGGAG
GTAGATGAGCAAATGCTCAATGTTCAAAATAAGAATAGTAGTTACTTTGTTGAATGGATCCCCAACAATGTGAAAACAGC
CATTTGTAACATCCCATCCCGGGGCCTGAAAATGTCTGCCACCTTCATTGGTAACAGTACTGCCATCCAAGAGCTCTTTA
AGCACATTTCTGAGCAGTTTACAGCCATGTTTCACAGAAAGGCTTTCTTACACTGGTATACTGGAGAGGGCATGGATGAA
ATGGAATTCACTGAAGCAGAAAGCAACATGAATGACTTGGTTTCTAAGTATCAGCAGTATCAGGATGCCACAGCTGAGGA
GGAGGGAAATTTTGAGGAGACTGAAGAGGAGGTGGAATAA

Alignment

ORF - retro_mdom_117 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.14 %
• Parental protein coverage: 99.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGKYVPRAVLVDLEP
          MREI..LQA.QC..QI..KFWEVISD.HGIDPT.TYHG.S.LQLERI..YYNEATGGKYVPRAVLVDLEP
Retrocopy MREIMPLQARQC--QISTKFWEVISDKHGIDPTRTYHGESNLQLERIHIYYNEATGGKYVPRAVLVDLEP

Parental  GTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
          GTMDSVRSGPFGQIFRPDNFVFGQS.AGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCL.GFQL.HSLG
Retrocopy GTMDSVRSGPFGQIFRPDNFVFGQSVAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLPGFQLMHSLG

Parental  GGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
          .GTGSGMGTLLISKIR....DRIMNTFSVV.SPKV.DTVVEPYNATLSVHQLVENTDETYCIDNEA.Y.I
Retrocopy VGTGSGMGTLLISKIRA---DRIMNTFSVVSSPKVLDTVVEPYNATLSVHQLVENTDETYCIDNEAFYNI

Parental  CFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQ
          CFRTLKLT.PTYGDLNH.VSATMSGVTTCL.FPGQLN.DL.KLAVN.V.FPRLHFFMPGFAPLT..GSQQ
Retrocopy CFRTLKLTSPTYGDLNHRVSATMSGVTTCLCFPGQLNIDLSKLAVNLVTFPRLHFFMPGFAPLTICGSQQ

Parental  YRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVK
          Y.ALTVPELTQQMFDAKNMMAACDP.HG.YLTVAAVFRG..SMKEVDEQMLNVQNKNSSYFVEWIPNNVK
Retrocopy YHALTVPELTQQMFDAKNMMAACDPWHGCYLTVAAVFRGHISMKEVDEQMLNVQNKNSSYFVEWIPNNVK

Parental  TAVCDIPPRGLKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
          TA.C.IP.RGLKMSATFIGNSTAIQELFK.ISEQFTAMF.RKAFLHWYTGEGMDEMEFTEAESNMNDLVS
Retrocopy TAICNIPSRGLKMSATFIGNSTAIQELFKHISEQFTAMFHRKAFLHWYTGEGMDEMEFTEAESNMNDLVS

Parental  EYQQYQDATAEEEGEFEEEAEE
          .YQQYQDATAEEEG.FEE..EE
Retrocopy KYQQYQDATAEEEGNFEETEEE

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	0.48 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	2.55 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_117 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_117 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016380	2 retrocopies	retro_amel_817, retro_amel_868,
Cavia porcellus	ENSCPOG00000011966	1 retrocopy	retro_cpor_497,
Microcebus murinus	ENSMICG00000010939	1 retrocopy	retro_mmur_792,
Macaca mulatta	ENSMMUG00000012164	2 retrocopies	retro_mmul_1849, retro_mmul_2533,
Monodelphis domestica	ENSMODG00000017213	1 retrocopy	retro_mdom_117 ,
Mus musculus	ENSMUSG00000036752	2 retrocopies	retro_mmus_158, retro_mmus_422,
Otolemur garnettii	ENSOGAG00000005927	2 retrocopies	retro_ogar_3410, retro_ogar_3450,
Pan troglodytes	ENSPTRG00000023373	2 retrocopies	retro_ptro_2403, retro_ptro_3166,
Rattus norvegicus	ENSRNOG00000010170	2 retrocopies	retro_rnor_742, retro_rnor_867,