RetrogeneDB ID: retro_mmus_1607

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:5110778..5112110(-)
• Located in intron of: ENSMUSG00000069729

Retrocopy information

• Ensembl ID: ENSMUSG00000081783
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tuba1b
• Ensembl ID: ENSMUSG00000023004
• Aliases: Tuba1b, Tuba2
• Description: tubulin, alpha 1B [Source:MGI Symbol;Acc:MGI:107804]

Sequence

>retro_mmus_1607
ATTCGTGAATGCATCTCCACCCACGTTGGCCAGGCTGGTGTTCAGATCGGCAATGCCTACTGGGAGCTCTACTGCCTGGA
ACATGGCATCTAACCTGATGGCCAGAAGCCAAGTGACAAGACCACTGGGGAGGAGATGACCCCTTCTATACCTTCTTCAG
CGTGGCAGGAGCTGGCAAGCATGTGACCCGGGCAGTGTTTGTAGAACTGGAACGCATAGTTACTGAAGTTCATCCTGGCA
CCTGCCGCCAGCTCCTTCACCCTGAGCAAGGCAAGGAAGATGCTGCCAATAACCATGCCCATGGCCACTATACTATTGGT
GAGGAGATCATTGACCTTGTCTTGGACAGCATTCACAAGCTGGCTGACCAGTGCATGGGTCTCCAGCGCTTCTTGGTTTT
CCAGAGCTTTGGCGGGGAACTGACTCTAGGTTCACCTCCCTGCTGATGGAGCAGCTCTCTGTTGATTACAGGAAGAAGTC
CAAGCTGGAGTTCTCCATTTACCCAGCCCCCCTCCCCTTCCAGGTTTCCACTGCTGTGGTTGAGCCCTACAATTCCATCC
TCACCACCCACACCACCCTGGAGCACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTGTTGTAGA
TACCTCGACATCAAGCTTCCAACCTACACCAACCTTAACCGCCTTACTAGCCAGAAACAGTGTCTTCCATCACTGTTTCC
AGCAAATTTGATGGGGCCCTGAATATTGATCTGACAAAATTCCAGACCAACCCAGTGCCCTACCCTCGCATTCACTTCCC
TCTGGCCACTTATGCCCCTGTCATCTCTGCTGAGAAAGCCTACCATGAGCAGCTTTCTGTAGCAGAGATCACCAATGTCT
GCTTTGAGCCAACCAACCAGATGGTGAAATGTGACGCTCACCATGGTAAATACATGGCTTGCTGCCTGCTGTACCATGGT
GATATGGTTCCCAAAAATGTCGATGCTGCCATTGCCACCATCCAGACCAAGCGCAGCATCCAGTTTGTGGACTGGTGCCC
CACTGGCTTCAAGGTTGGCATTAATTACCAGCCTCCCACTGTGGTACCCGGTGGTGACCTGGCCAAGGTCCAGAGAGCTG
TGTGCATGGTGAGCAACACCACAGCCATTGCTGAGGCCTGGGCTCGCCTAGATCACAAGTTTGATCTGATGTATGCCAAG
CGTGCCTTTGTGCACTGGTATGTGGATGAGGGCATAGAGGAAGAGGAGTTCTCTGAGGCCCATGAGAACATGGCTGCCCT
AGAGAAGGATTATGAGGAGGCTGGTGTGGATTGTGTGGAAGGCGAGAGGGAG

Alignment

ORF - retro_mmus_1607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.96 %
• Parental protein coverage: 98.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIG-GGDDSFNTFFSETGAGKHVPRAVFVD
          .RECIS.HVGQAGVQIGNA.WELYCLEHGI.PDGQ.PSDKT.G.GGDD.F.TFFS..GAGKHV.RAVFV.
Retrocopy IRECISTHVGQAGVQIGNAYWELYCLEHGI*PDGQKPSDKTTG<GGDDPFYTFFSVAGAGKHVTRAVFVE

Parental  LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFH
          LE.....EV..GT.RQL.HPEQ...GKEDAANN.A.GHYTIG.EIIDLVLD.I.KLADQC.GLQ.FLVF.
Retrocopy LE-RIVTEVHPGTCRQLLHPEQ---GKEDAANNHAHGHYTIGEEIIDLVLDSIHKLADQCMGLQRFLVFQ

Parental  SFGG-GTGSGFTSLLMERLSVDYGKKSKLEFSIYPAP---QVSTAVVEPYNSILTTHTTLEHSDCAFMVD
          SFGG.GT.S.FTSLLME.LSVDY.KKSKLEFSIYPAP...QVSTAVVEPYNSILTTHTTLEHSDCAFMVD
Retrocopy SFGG<GTDSRFTSLLMEQLSVDYRKKSKLEFSIYPAPLPFQVSTAVVEPYNSILTTHTTLEHSDCAFMVD

Parental  NEAIYDICRRNLDIERPTYTN-LNRLIS-QIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYA
          NEAIYDIC.R.LDI..PTYTN.L..L.....VSSIT.S..FDGALN.DLT.FQTN.VPYPRIHFPLATYA
Retrocopy NEAIYDICCRYLDIKLPTYTN>LTALLA>ETVSSITVSSKFDGALNIDLTKFQTNPVPYPRIHFPLATYA

Parental  PVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQF
          PVISAEKAYHEQLSVAEITN.CFEP.NQMVKCD..HGKYMACCLLY.GD.VPK.V.AAIATI.TKRSIQF
Retrocopy PVISAEKAYHEQLSVAEITNVCFEPTNQMVKCDAHHGKYMACCLLYHGDMVPKNVDAAIATIQTKRSIQF

Parental  VDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGM
          VDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCM.SNTTAIAEAWARLDHKFDLMYAKRAFVHWYV.EG.
Retrocopy VDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMVSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVDEGI

Parental  EEGEFSEAREDMAALEKDYEEVGVDSVEGEGE
          EE.EFSEA.E.MAALEKDYEE.GVD.VEGE.E
Retrocopy EEEEFSEAHENMAALEKDYEEAGVDCVEGERE

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	0.19 RPM	77.45 RPM
SRP007412_cerebellum	0.04 RPM	63.92 RPM
SRP007412_heart	0.16 RPM	36.14 RPM
SRP007412_kidney	0.10 RPM	16.90 RPM
SRP007412_liver	0.05 RPM	8.82 RPM
SRP007412_testis	0.09 RPM	8.14 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1607 was not detected

EST

No EST(s) were mapped for retro_mmus_1607 retrocopy.

TSS

No TSS is located nearby retro_mmus_1607 retrocopy 5' end.

Lab

retro_mmus_1607 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1607 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 29 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,
Mus musculus	ENSMUSG00000023004	6 retrocopies	retro_mmus_1562, retro_mmus_1607 , retro_mmus_1742, retro_mmus_1987, retro_mmus_3297, retro_mmus_3327,
Mus musculus	ENSMUSG00000043091	1 retrocopy	retro_mmus_843,
Mus musculus	ENSMUSG00000067338	1 retrocopy	retro_mmus_3356,
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,