RetrogeneDB ID: retro_btau_436

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:45757733..45758306(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP3S2
• Ensembl ID: ENSBTAG00000001407
• Aliases: None
• Description: AP-3 complex subunit sigma-2 [Source:UniProtKB/Swiss-Prot;Acc:Q1JQA3]

Sequence

>retro_btau_436
ATCAAGGCGATCCTCATCTTTAACAACCACGGGAAGCCGCGGCTCTCCAAGTTCTACCAGCCCTACAGTGAAGATACACA
ACAGCAAATCATCAGGGAGACATTCCATTTGGTATCTAAGAGAGATGAAAATGTTTGTAATTTCCTAGAAGGAGGATTAT
TAATTGGAGGATCCGACAACAAACTGATTTATAGACATTATGCAACATTATATTTTGTCTTCTGTGTGGATTCTTCAGAA
AGTGAACTTGGCATTTTAGATTTAATTCAAGTATTTGTGGAAACATTAGACAAGTGTTTTGAAAACGTCTGTGAACTGGA
TTTAATTTTCCATGTAGACAAGGTTCACAATATTCTTGCAGAAATGGTGATGGGGTGAATGGTACTGGAGACCAACATGA
ATGAGATTGTTACACAAATTGATGCACAGAATAAACTGGAGAAATCTGAGGCTGGCTTAGCAGGAGCTCCAGCCCGTGCT
GTATCAGCTGTAAAGAATATGAATCTTCCTGAGATCCCAAGAAATATTAACATTGGTGACATCAGTATAAAAGTGCCAAA
CCTACCCTCTTTT

Alignment

ORF - retro_btau_436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.25 %
• Parental protein coverage: 98.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IQAILVFNNHGKPRLVRFYQRFPEEIQQQIVRETFHLVLKRDDNICNFLEGGSLIGGSDYKLIYRHYATL
          I.AIL.FNNHGKPRL..FYQ...E..QQQI.RETFHLV.KRD.N.CNFLEGG.LIGGSD.KLIYRHYATL
Retrocopy IKAILIFNNHGKPRLSKFYQPYSEDTQQQIIRETFHLVSKRDENVCNFLEGGLLIGGSDNKLIYRHYATL

Parental  YFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHMDKVHYILQEVVMGGMVLETNMNEIVAQI
          YFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFH.DKVH.IL.E.VMG.MVLETNMNEIV.QI
Retrocopy YFVFCVDSSESELGILDLIQVFVETLDKCFENVCELDLIFHVDKVHNILAEMVMG*MVLETNMNEIVTQI

Parental  EAQNRLEKSEGGLSAAPARAVSAVKNINLPEMPRNINIGDLNIKVPNLSQF
          .AQN.LEKSE.GL..APARAVSAVKN.NLPE.PRNINIGD..IKVPNL..F
Retrocopy DAQNKLEKSEAGLAGAPARAVSAVKNMNLPEIPRNINIGDISIKVPNLPSF

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	1.95 RPM	7.35 RPM
ERP005899_muscle	8.29 RPM	31.78 RPM
SRP017611_brain	6.85 RPM	33.48 RPM
SRP017611_kidney	2.19 RPM	48.25 RPM
SRP017611_liver	1.89 RPM	21.14 RPM
SRP030211_testis	17.05 RPM	21.58 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_436 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_436 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_436 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001407	1 retrocopy	retro_btau_436 ,
Choloepus hoffmanni	ENSCHOG00000003359	4 retrocopies	retro_chof_1775, retro_chof_194, retro_chof_434, retro_chof_88,
Dipodomys ordii	ENSDORG00000004247	1 retrocopy	retro_dord_115,
Equus caballus	ENSECAG00000024044	1 retrocopy	retro_ecab_549,
Felis catus	ENSFCAG00000028122	1 retrocopy	retro_fcat_311,
Macropus eugenii	ENSMEUG00000003421	1 retrocopy	retro_meug_2032,
Monodelphis domestica	ENSMODG00000019522	1 retrocopy	retro_mdom_316,
Nomascus leucogenys	ENSNLEG00000011780	2 retrocopies	retro_nleu_1380, retro_nleu_1555,
Otolemur garnettii	ENSOGAG00000030982	1 retrocopy	retro_ogar_1737,
Rattus norvegicus	ENSRNOG00000043141	1 retrocopy	retro_rnor_931,
Sus scrofa	ENSSSCG00000030174	7 retrocopies	retro_sscr_1109, retro_sscr_199, retro_sscr_268, retro_sscr_339, retro_sscr_620, retro_sscr_721, retro_sscr_753,
Tursiops truncatus	ENSTTRG00000015554	2 retrocopies	retro_ttru_1233, retro_ttru_1361,
Vicugna pacos	ENSVPAG00000008668	1 retrocopy	retro_vpac_54,