RetrogeneDB ID: retro_sscr_380

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 13:105966027..105966771(-)
• Located in intron of: None

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_380
CAGATACCAAGTAACAAGACCCCTGGGGGAGGAGATGACTCCTTCAACACCTTCTTTAAGTGAGATAGGAGCTGGCAAGC
ATGTGCCCAGGGCAGGTTTGTAGACCTGGAACCCACAGTCATTGATGAAGTTAGCACTGGCACCTACTGCCTGCTCTTCC
ACCCTGAGCAGCTCATCACAGGCAAAAAAGATGCTGCCAATAACTATTCCAGAAGTCACTATCCCATTGGCAAGGAGATC
ATTGACCTCATCTTGGACCCAGTTCAGAACTGGCTGACCAGTGCACAGGTCTTCAGGGCTTCTTGGTTTTCCACAGCTTT
GGTTGGGGAAACTGGTTCTGGGTTCACCTCTCTGCTGATGGAACGTTTCTCTGTCGATTATGGGAATAAGTCCAAGCTGG
AATTCTCCATTTATTCAGCCCCCTAGGTTTCCACAGCTGTAGGTGAGCCTTACATTTCCATCCTTACCACCCACACCACC
GTGGAGAACTCTGATTGTGCCTTCATGGTAGACAATGAGGCCATCTATGACATCTTTCATAGAAACCTTGATATTGAGCA
CCCATCCTACACTACTCTGAACCACCTCATTAGCCAGATTGTGTCCTCCATCACTGCTTCTCTGAGGTTTGATGGAGCCA
TGAATGTTGATCTGACAGAATTCCAGACCAGCTTGTTGCCCTACTCCTGCATCCATTTCCCTCTGGCCACATATGCCCCT
GTCATCTCTGCTGAGAAAGTCTAC

Alignment

ORF - retro_sscr_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 54.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QMPSDKTIGGGDDSFNTFF-SETGAGKHVPRAV-FVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANN
          Q.PS.KT.GGGDDSFNTFF.SE.GAGKHVPRA..FVDLEPTVIDEV.TGTY..LFHPEQLITGK.DAANN
Retrocopy QIPSNKTPGGGDDSFNTFF>SEIGAGKHVPRAG<FVDLEPTVIDEVSTGTYCLLFHPEQLITGKKDAANN

Parental  YARGHYTIGKEIIDLVLDRIR-KLADQCTGLQGFLVFHSFGGG-TGSGFTSLLMERLSVDYGKKSKLEFS
          Y.R.HY.IGKEIIDL.LD.....LADQCTGLQGFLVFHSFG.G.TGSGFTSLLMER.SVDYG.KSKLEFS
Retrocopy YSRSHYPIGKEIIDLILDPVQ<ELADQCTGLQGFLVFHSFGWG>TGSGFTSLLMERFSVDYGNKSKLEFS

Parental  IYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
          IY.AP.VSTAV.EPY.SILTTHTT.E.SDCAFMVDNEAIYDI..RNLDIE.P.YT.LN.LISQIVSSITA
Retrocopy IYSAP*VSTAVGEPYISILTTHTTVENSDCAFMVDNEAIYDIFHRNLDIEHPSYTTLNHLISQIVSSITA

Parental  SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAY
          SLRFDGA.NVDLTEFQT.L.PY..IHFPLATYAPVISAEK.Y
Retrocopy SLRFDGAMNVDLTEFQTSLLPYSCIHFPLATYAPVISAEKVY

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	0.00 RPM	764.13 RPM
SRP014902_testis	0.00 RPM	814.59 RPM
SRP018288_heart	0.00 RPM	214.81 RPM
SRP018288_kidney	0.00 RPM	190.81 RPM
SRP018288_liver	0.00 RPM	79.95 RPM
SRP018288_lung	0.00 RPM	415.86 RPM
SRP018856_adipose	0.00 RPM	302.94 RPM
SRP035408_brain	0.00 RPM	182.11 RPM
SRP035408_liver	0.00 RPM	29.41 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_380 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_380 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_380 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,