RetrogeneDB ID: retro_btau_371

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 10:37115368..37115818(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNAP23
• Ensembl ID: ENSBTAG00000005661
• Aliases: None
• Description: synaptosomal-associated protein 23 [Source:RefSeq peptide;Acc:NP_001069299]

Sequence

>retro_btau_371
AATAAAGACATGAGAGAAGCAGAGAAGATTTTAACAGAATTCAACAAGGACTGAGGCCGTTGTTTATGTCCATGTAATAG
GACAAAGAACATTGAGTCTGGTAAAGTCTATAAGGCAACATGGGGAGATGCTGGAGACAGCTCTCCTAGCAATGTAATAG
TATCTAAGCAGCCAGGCTGAGTGACAAATGGTCAGCTGCGTCAAGTGACCACAGGAGCAGCCAACGGGTGAATACATTAA
ACATATAACAAATCATGCCAGGGAAGATGAAACGGAAGAGAACCTGACTCAAGTGGCCAGTATCCTAGACAACCTAAAAA
CATGGCCCTGGACATAGGCAATGGGATTGAGGCTCACAACTGACAAATAGAACAGATCACAGAAAAGGCTGACACCAATA
AAGATCATATTGATAATGCCAATGCCAGGGCAAAGAAACTCACTGACAGC

Alignment

ORF - retro_btau_371 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.32 %
• Parental protein coverage: 70.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NEDMREAEKTLTELNKCCGLCVCPCSRTKNFESSKAYKATWGDGGDNSPSN-IVSKQPGRVTNGQPQQAT
          N.DMREAEK.LTE.NK..G.C.CPC.RTKN.ES.K.YKATWGD.GD.SPSN.IVSKQPG.VTNGQ..Q.T
Retrocopy NKDMREAEKILTEFNKD*GRCLCPCNRTKNIESGKVYKATWGDAGDSSPSNVIVSKQPG*VTNGQLRQVT

Parental  AGAA-SGGYIKRITNDAREDEMEDNLTQVGSILGNL-KNMALDMGNEIEAQNRQIERITEKADTNKDRID
          .GAA..G.YIK.ITN.AREDE.E.NLTQV.SIL.NL.KNMALD.GN.IEA.N.QIE.ITEKADTNKD.ID
Retrocopy TGAA>TGEYIKHITNHAREDETEENLTQVASILDNL<KNMALDIGNGIEAHN*QIEQITEKADTNKDHID

Parental  NANARAKKLIDS
          NANARAKKL.DS
Retrocopy NANARAKKLTDS

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
ERP005899_liver	0.00 RPM	42.46 RPM
ERP005899_muscle	0.00 RPM	36.69 RPM
SRP017611_brain	0.00 RPM	8.59 RPM
SRP017611_kidney	0.00 RPM	70.47 RPM
SRP017611_liver	0.00 RPM	17.59 RPM
SRP030211_testis	0.04 RPM	13.99 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_371 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_371 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_371 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015685	1 retrocopy	retro_acar_38,
Ailuropoda melanoleuca	ENSAMEG00000015774	1 retrocopy	retro_amel_206,
Bos taurus	ENSBTAG00000005661	2 retrocopies	retro_btau_1622, retro_btau_371 ,
Canis familiaris	ENSCAFG00000011105	2 retrocopies	retro_cfam_1073, retro_cfam_1780,
Choloepus hoffmanni	ENSCHOG00000006468	3 retrocopies	retro_chof_1, retro_chof_1652, retro_chof_1784,
Cavia porcellus	ENSCPOG00000003638	1 retrocopy	retro_cpor_862,
Felis catus	ENSFCAG00000013387	1 retrocopy	retro_fcat_1114,
Loxodonta africana	ENSLAFG00000005462	1 retrocopy	retro_lafr_839,
Microcebus murinus	ENSMICG00000000813	2 retrocopies	retro_mmur_1188, retro_mmur_377,
Monodelphis domestica	ENSMODG00000017889	1 retrocopy	retro_mdom_1772,
Mustela putorius furo	ENSMPUG00000009856	3 retrocopies	retro_mputfur_1181, retro_mputfur_692, retro_mputfur_915,
Mus musculus	ENSMUSG00000027287	1 retrocopy	retro_mmus_2570,
Rattus norvegicus	ENSRNOG00000050552	2 retrocopies	retro_rnor_1505, retro_rnor_2389,
Tarsius syrichta	ENSTSYG00000006589	2 retrocopies	retro_tsyr_1020, retro_tsyr_715,
Tursiops truncatus	ENSTTRG00000002561	1 retrocopy	retro_ttru_658,