RetrogeneDB ID: retro_sscr_702

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 3:49835733..49836566(+)
• Located in intron of: ENSSSCG00000023884

Retrocopy information

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

Parental gene information

• Parental gene symbol: TUBA1B
• Ensembl ID: ENSSSCG00000000190
• Aliases: TUBA1B, TUBA3
• Description: Sus scrofa tubulin, alpha 1b (TUBA1B), mRNA. [Source:RefSeq mRNA;Acc:NM_001044544]

Sequence

>retro_sscr_702
AACGTGCCCAGGGCAGTGTTAGTCAACCTGGAACCCTCAATCATTGATGACGTTTGCACTGGCACCTACGCCAGCTCCTC
CACCGTGAGCATCTCATCACAGGCAAGGAAGATGGTACCGATAACCACGCCCCGGGTCACCACACCATTGGTACTGAGAT
CATTGACCGTGTCTTGGACCCAGTGTAGAAGCTGGCTGACTGGTGCACATGCCTCCAGGGCTTCTTGGTTTTCCACAGCT
CTGGTGGGGGAACTGATTCTGGGTTCACCTTCCTGCTTATGGGACGTCTCTCTGTCGATTATGGCAAGAAGTCCAAGCTG
GAGGTCTCCATTTACCCAGCCCCCCAGGTTTGCACTGCTGTAGTTGAGCCCTACAACTCCATCCTCTCCACCCACACCAC
CCAGGAGCACTCTGATTGTGCCTTCATGGTAGGCCACAAGTCCATCTATGACATCTGTGGTAGAAAACACGATATTGAGC
GCCCAACCTACACTCCTCTGAACCTCGTCATTAGCTGATTGTGTCCTCCATCACTGCTTCCCTGGGGTTGGGTGGAGCCC
TGAACGTTGATCTGACAGAATGCCAGACCACCTTGATGCCCTGTCGCTGCATCCATTTCCCTCTTTCCACTTAGGCCCTG
TCATCTCTGCTGAGAAAGCCTACCATGAACAGCTTTCTGTAGCAGAGATCACTAATGCTTGGTTAGAGCCAGCCAACCAG
ATGGTGAAGTATGACCCTTACCATGGAAACACATGGCTTACTGCTGGTCGTACTGCACCGATGTGATTCCCAAAGACATC
GATGCTGCCATCGCCACCTTTAAGACCAAGCGT

Alignment

ORF - retro_sscr_702 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.91 %
• Parental protein coverage: 61.86 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HVPRAVFVDLEPTVIDEVRTGTY-RQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQC
          .VPRAV.V.LEP..ID.V.TGTY.RQL.H.E.LITGKED...N.A.GH.TIG.EIID.VLD...KLAD.C
Retrocopy NVPRAVLVNLEPSIIDDVCTGTY<RQLLHREHLITGKEDGTDNHAPGHHTIGTEIIDRVLDPV*KLADWC

Parental  TGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSD
          T.LQGFLVFHS.GGGT.SGFT.LLM.RLSVDYGKKSKLE.SIYPAPQV.TAVVEPYNSIL.THTT.EHSD
Retrocopy TCLQGFLVFHSSGGGTDSGFTFLLMGRLSVDYGKKSKLEVSIYPAPQVCTAVVEPYNSILSTHTTQEHSD

Parental  CAFMVDNEAIYDICRRNLDIERPTYTNLNRLIS-QIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFP
          CAFMV....IYDIC.R..DIERPTYT.LN..IS..IVSSITASL...GALNVDLTE.QT.L.P...IHFP
Retrocopy CAFMVGHKSIYDICGRKHDIERPTYTPLNLVIS<LIVSSITASLGLGGALNVDLTECQTTLMPCRCIHFP

Parental  LATYA-PVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRHG-KYMACCLLYRGDVVPKDVNAAIATIK
          L.T.A.PVISAEKAYHEQLSVAEITNA..EPANQMVK.DP.HG.K.MA.C..Y..DV.PKD..AAIAT.K
Retrocopy LST*A<PVISAEKAYHEQLSVAEITNAWLEPANQMVKYDPYHG<KHMAYCWSYCTDVIPKDIDAAIATFK

Parental  TKR
          TKR
Retrocopy TKR

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
SRP014902_placenta	0.66 RPM	764.13 RPM
SRP014902_testis	1.13 RPM	814.59 RPM
SRP018288_heart	0.18 RPM	214.81 RPM
SRP018288_kidney	0.20 RPM	190.81 RPM
SRP018288_liver	0.00 RPM	79.95 RPM
SRP018288_lung	0.20 RPM	415.86 RPM
SRP018856_adipose	0.08 RPM	302.94 RPM
SRP035408_brain	0.35 RPM	182.11 RPM
SRP035408_liver	0.09 RPM	29.41 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_702 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_702 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_702 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 27 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,
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 ,