RetrogeneDB ID: retro_ecab_270

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 11:60508261..60509389(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAT
• Ensembl ID: ENSECAG00000023644
• Aliases: None
• Description: amidophosphoribosyltransferase [Source:RefSeq peptide;Acc:NP_001098786]

Sequence

>retro_ecab_270
GGGAAAATAGCTGTGGCACATAATGGCGAATTGATAAATGCTGCTCAATTAAGGGAAAAGCTTCTGCGTCATGGTATTGG
TCTGTCAAGAAGTTCCGATAGGGAAATGATTACCCAGTTACTGGCATATACCTCACCTCAGGAACAAGATGACACCCCAG
ACTGGGTGGCAAGGATTAAAAACTTAATGAAGGAAGCACCTACAGCATACTCCCTGCTTATAATGCACAGAGATGTTATT
TATGCAGTACGAGATCCTTATGGAAATTGTCCTCTATGCATTGGTCGTCTTATTCCTATATCTGATATAAATGATAAAGA
GAAAAACTCTTCAGAAACCGAAGGATGGGCGGTATCTTCAGAACCTTGTAGCTTTTTATCTGTTGGTGCAAGATATTACC
GTGAAGTCTTACCTGGAGAAATTGTGAAAATATCCAGACATAATGTCCAAACACTTGATACTATACCAAGGTCTGAAGGA
AAACCAATGGCTTTTTGTATTTTTGAATATGTTTATTTTGCAAGACCAGATAGTATATTTGAAATCCAAATGGTTTATAC
AGTGAGGTACTGTTGTGGTCAGCAGCTGGCAATTGAACCACCTGTGGATGCAGATTTGGTTAGCACCGTTCTGAATCTGC
TACACCCGCTGCTCTTGGTTATGCAGGAAGGTGTGGGCTTCCCTATGTGGAGGTGCTGTGTAAAACCCGGTATGTAGGAA
GAACCTTCATTCAGCCAAACATGAAGTTAAGACAACTTAGTGTTGCAAAAAAAATTTGGAGTAGTGTCAGACAACTTCAA
AGGCAAAGGAATTGTTCTTGTAGATGATTGGATTGTAAGAGACAATATGACCTCACCCATAATCAAATTGCTCAAAGAAT
CTGGTGCAAAAGAGGTACACATTTGAGTAACTTCACCACCAATTAGATATCCATGCTTCATGGGAATAAACATACCAGCA
AAAGAAGAGCTTTTGCCAATAAAGCAGAATTTGAACATCTTGCAGAATATCTAGGAGCAAACAGTGTTGTGTATCTGTCA
GTAGAAGGACTGGTTTCATCTGTACGAGAAGGGATAAAACAAAGAATAGAAAGAGAAAATGCAAGATATTATGATTCAAG
AAAATGGG

Alignment

ORF - retro_ecab_270 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.96 %
• Parental protein coverage: 72.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GKIAVAHNGELINAAHLRRKLLRHGIGLSTSSDSEMITQLLAYTPPQEQDDTPDWVARIKNLMKEAPTAY
          GKIAVAHNGELINAA.LR.KLLRHGIGLS.SSD.EMITQLLAYT.PQEQDDTPDWVARIKNLMKEAPTAY
Retrocopy GKIAVAHNGELINAAQLREKLLRHGIGLSRSSDREMITQLLAYTSPQEQDDTPDWVARIKNLMKEAPTAY

Parental  SLLIMHRDVIYAVRDPYGNRPLCIGRLIPISDINDKEKKSSETEGWVVSSESCSFLSIGARYYREVLPGE
          SLLIMHRDVIYAVRDPYGN.PLCIGRLIPISDINDKEK.SSETEGW.VSSE.CSFLS.GARYYREVLPGE
Retrocopy SLLIMHRDVIYAVRDPYGNCPLCIGRLIPISDINDKEKNSSETEGWAVSSEPCSFLSVGARYYREVLPGE

Parental  IVEISRHNVQTLDIIPRSEGNPMAFCIFEYVYFARPDSIFENQMVYTVRYRCGQQLAIEAPVDADLVSTV
          IV.ISRHNVQTLD.IPRSEG.PMAFCIFEYVYFARPDSIFE.QMVYTVRY.CGQQLAIE.PVDADLVSTV
Retrocopy IVKISRHNVQTLDTIPRSEGKPMAFCIFEYVYFARPDSIFEIQMVYTVRYCCGQQLAIEPPVDADLVSTV

Parental  -PESATPAALGYAGKCGLPYVEVLCKNRYVGRTFIQPNMRLRQLGV-AKKFGVLSDNFKDKRIVLVDDSI
          ..ESATPAALGYAG.CGLPYVEVLCK.RYVGRTFIQPNM.LRQL.V....FGV.SDNFK.K.IVLVDD.I
Retrocopy <SESATPAALGYAGRCGLPYVEVLCKTRYVGRTFIQPNMKLRQLSV>XXXFGVVSDNFKGKGIVLVDDWI

Parental  VRGNTISPIIKLLKESGAKEVHIRVASPPIRYPCFMGINIPTKEELI-ANKPEFEHLAEYLGANSVVYLS
          VR.N..SPIIKLLKESGAKEVHI.V.SPPIRYPCFMGINIP.KEEL..ANK.EFEHLAEYLGANSVVYLS
Retrocopy VRDNMTSPIIKLLKESGAKEVHI*VTSPPIRYPCFMGINIPAKEELL<ANKAEFEHLAEYLGANSVVYLS

Parental  VEGLVSSVREGI-KLKKKK-EKKQDIIIQENG
          VEGLVSSVREGI.K.K..K.EK.QDI.IQENG
Retrocopy VEGLVSSVREGI<KTKNRK<EKMQDIMIQENG

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
SRP021940_articular_cartilage	0.00 RPM	4.84 RPM
SRP021940_cerebellum	0.00 RPM	7.11 RPM
SRP021940_embryo	0.08 RPM	16.24 RPM
SRP021940_placental_villous	0.00 RPM	9.19 RPM
SRP021940_synovial_membrane	0.03 RPM	5.00 RPM
SRP021940_testis	0.00 RPM	7.55 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_270 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_270 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_270 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000023644	2 retrocopies	retro_ecab_1113, retro_ecab_270 ,
Homo sapiens	ENSG00000128059	1 retrocopy	retro_hsap_2809,
Gorilla gorilla	ENSGGOG00000004608	1 retrocopy	retro_ggor_1953,
Monodelphis domestica	ENSMODG00000020693	1 retrocopy	retro_mdom_1487,
Nomascus leucogenys	ENSNLEG00000008762	1 retrocopy	retro_nleu_431,
Pongo abelii	ENSPPYG00000029568	1 retrocopy	retro_pabe_2306,
Pan troglodytes	ENSPTRG00000016080	1 retrocopy	retro_ptro_1903,
Tursiops truncatus	ENSTTRG00000010928	1 retrocopy	retro_ttru_794,