RetrogeneDB ID: retro_ecab_1113

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:58513978..58514755(-)
• 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_1113
TTATGCACTAGTCATCTCATTCCTGTGACTGACGTAAATGGAAAAAGGAAATAAAAATCCTACAGAAACAGAAGGGTGTG
TGGTGATTTCAGAATCTTGTAACTTTTTATCTATTGGTATGTATTGCCATGAAGTCTTTCCTAGAGAAATTATGAAAATA
TCTAGACATTATGTCTAAACTTTCAATATTATATTAAGGTCTGAAGGAAATTTGACGTCTCTTTGTATGTTTGAATAGGC
TTATTTTGCAAAACCAGATGGTATATTTGAAGAGCAAATAGTAAGATATCATTGTTGTCAGCAACTGGCAATTTAAGCAC
CTGTAAAGAGGAGTTGGTGAGCACATTTCCCAAATTTGCTGTGCCTGCTGCTCCTGGTTAGTCAGAAAAATGTACATTTC
CCTATGTGAAGGTGCTGTATAAAAGCTGGTAGTTAGGAATAACTCTCATCCAGCTAATATGAGATTAAGAGAACTTGGTG
TTGAAAAATGAAATTGAAATATTATCAGACAACTTAATAGGTGAAAGAATTGTTCCTATAGATGATTAACTTGCAAGAGA
CAATATCATACCGCCCATAACAAAATTTCTCAAAGAATCTCATGCAAAAGAAATGCAAACTTGAGTAGCTTCATCACCAA
TATGATTTCCGTGCTTCATGAGAATAGACATTTCCACAAAAGAGGAGCTTATTGCCAATAAATTTGATCATTTCGCATAA
TATCTGGGAGCAAAGAGCATCACGTATCTGTCACTAGAAGTACTGTTTTCATCTATC

Alignment

ORF - retro_ecab_1113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.36 %
• Parental protein coverage: 50.67 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LCIGRLIPISDINDKEK-KS-SETEGWVVSSESCSFLSIGARYYREVLPGEIVEISRHNVQTLDIIPRSE
          LC...LIP..D.N.K.K.KS..ETEG.VV.SESC.FLSIG..Y..EV.P.EI..ISRH.V.T..II.RSE
Retrocopy LCTSHLIPVTDVNGKRK*KS>TETEGCVVISESCNFLSIGM-YCHEVFPREIMKISRHYV*TFNIILRSE

Parental  GNPMAFCIFEYVYFARPDSIFENQMVYTVRYRCGQQLAIEAPVDA-DLVSTVPESATPAALGYAGKCGLP
          GN....C.FE..YFA.PD.IFE.Q....VRY.C.QQLAI.APV....LVST.P..A.PAA.G...KC..P
Retrocopy GNLTSLCMFE*AYFAKPDGIFEEQI---VRYHCCQQLAI*APVKR<ELVSTFPKFAVPAAPG*SEKCTFP

Parental  YVEVLCKNRYVGRTFIQ-PNMRLRQLGVAK-KFGVLSDNFKDKRIVLVDDSIVRGNTISPIIKLLKESGA
          YV.VL.K....G.T.IQ..NMRLR.LGV.K.....LSDN....RIV..DD...R.N.I.PI.K.LKES.A
Retrocopy YVKVLYKSW*LGITLIQ<ANMRLRELGVEK>EIEILSDNLIGERIVPIDD*LARDNIIPPITKFLKESHA

Parental  KEVHIRVASPPIRYPCFMGINIPTKEELIANKPEFEHLAEYLGANSVVYLSVEGLVSSV
          KE....VAS.PI..PCFM.I.I.TKEELIANK..F.H.A.YLGA.S..YLS.E.L.SS.
Retrocopy KEMQT*VASSPI*FPCFMRIDISTKEELIANK--FDHFA*YLGAKSITYLSLEVLFSSI

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	0.00 RPM	16.24 RPM
SRP021940_placental_villous	0.00 RPM	9.19 RPM
SRP021940_synovial_membrane	0.00 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_1113 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1113 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1113 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,