RetrogeneDB ID: retro_btau_1293

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 3:94843183..94843615(-)
• Located in intron of: ENSBTAG00000011025

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1AX
• Ensembl ID: ENSBTAG00000017633
• Aliases: None
• Description: eukaryotic translation initiation factor 1A, X-chromosomal [Source:RefSeq peptide;Acc:NP_001020500]

Sequence

>retro_btau_1293
ATGCCTAAGAATAAAGGTAAAGAAGGTAAAAACAGACGCAGAGGCAAGAATGAGAATGAACCTGAAAAGAGGGCGCTAGT
GTTCAAAGAAGATGAGCAAGAGTATGCCCAAGTAATCAAAATGTTGGGAAACGGACGATTGGAAGCTATGTGTTTCGATG
GTGTTAAGAGATTGTACCACATCAGAGGGAAACTGAGAAAGAAGGTCTGGATAAATACCTCAGACATTATATTGGTTGGT
CTTCGGGACTACCAGGATAATAATAAAGCTGATGTAATCTTAAAATACAATGCAGATAAGGCTAGAAGTCTGAAGGCATA
TGGCAAGCTTCCAGAAAATGCTAAAATCAATGAAACTGATACATTTGGCTCTGGAGATGATGAAATCCAGTTTGATGACA
TTGGAGATGATGATGGAGACATTGATGATATC

Alignment

ORF - retro_btau_1293 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVW
          MPKNKGK.GKNRRRGKNENE.EKR.LVFKED.QEYAQVIKMLGNGRLEAMCFDGVKRL.HIRGKLRKKVW
Retrocopy MPKNKGKEGKNRRRGKNENEPEKRALVFKEDEQEYAQVIKMLGNGRLEAMCFDGVKRLYHIRGKLRKKVW

Parental  INTSDIILVGLRDYQDN-KADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDEIQFDDIGDDDE
          INTSDIILVGLRDYQDN.KADVILKYNAD.ARSLKAYG.LPE.AKINETDTFG.G.DDEIQFDDIGDDD.
Retrocopy INTSDIILVGLRDYQDNNKADVILKYNADKARSLKAYGKLPENAKINETDTFGSG-DDEIQFDDIGDDDG

Parental  DIDDI
          DIDDI
Retrocopy DIDDI

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	1.08 RPM	43.69 RPM
ERP005899_muscle	0.42 RPM	103.20 RPM
SRP017611_brain	0.73 RPM	29.69 RPM
SRP017611_kidney	0.41 RPM	65.08 RPM
SRP017611_liver	0.38 RPM	24.84 RPM
SRP030211_testis	1.26 RPM	116.93 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1293 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1293 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1293 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017633	3 retrocopies	retro_btau_1293 , retro_btau_293, retro_btau_381,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Erinaceus europaeus	ENSEEUG00000007518	3 retrocopies	retro_eeur_408, retro_eeur_567, retro_eeur_686,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pongo abelii	ENSPPYG00000020176	1 retrocopy	retro_pabe_1185,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sorex araneus	ENSSARG00000013528	1 retrocopy	retro_sara_324,
Sarcophilus harrisii	ENSSHAG00000010995	1 retrocopy	retro_shar_707,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Tursiops truncatus	ENSTTRG00000002012	1 retrocopy	retro_ttru_1009,
Vicugna pacos	ENSVPAG00000009927	4 retrocopies	retro_vpac_47, retro_vpac_531, retro_vpac_550, retro_vpac_590,