RetrogeneDB ID: retro_ecab_942

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 7:92666093..92666782(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAE1
• Ensembl ID: ENSECAG00000021954
• Aliases: None
• Description: NEDD8 activating enzyme E1 subunit 1 [Source:HGNC Symbol;Acc:621]

Sequence

>retro_ecab_942
ATGAATTTCTTACAGGAATTAAATAACAATGGATCTGGAAGGCTGTGGACGAAAGTTCAGAAAACCTTCTAAACAATGAC
CTTTCTTCTTCCTGTAGATTTACCGCTGTGGTTGCACCTAGGCTCCCTGAAAGTACATTACTATATTTAGCTGATGTCCT
CCAGAATTCTCAAATCTCCCTTTTAATCTATGGGACATACATGGCTTTTGGCGATAGGAGGAACATTATAAAAGAACATC
CGGTAATAGAATTTCACCAAGATAAAACAAAGAAGATCTACAACTGGATAAACCGTTTCTGAACTGAGAGAACATTTTCA
ATCTTACAGTTTGGATTATACAGGAAAAGACAAGACCATAGCAACACTGTAGATTGTGATCATAGCTAAATATTTAGCAT
AGTGGAATAGTGACACAAATGGATGAACACCCAAAATGTGTCAAGGAAAAGAAGACTTCAGAGATTTGATCAGACCAGGG
ATTCTAAAGAATGAAATGAGGGCTCCAGAAGATGAAGAGAATTTTGAGGAAGCTATTAAAAATATAAACACAGCAATAAA
TACAGCTCAGATCCCAATCAATATTAAAGATATTTTAATGAGAATTGCTGCATAAATATCAGCCAACAGACTCCATTCTT
TTAGCTTTTAGCTTATGCCTTAAAGGACTTTGTGGACAAAGAGGCACAA

Alignment

ORF - retro_ecab_942 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.96 %
• Parental protein coverage: 51.91 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEFLQELNNDVSGSF-VEESPENLLDNDPSFFCRFTIVVATQLPESTLLRLADVLWNSQIPLLVCRTYGL
          M.FLQELNN..SG...V.ES.ENLL.ND.S..CRFT.VVA..LPESTLL.LADVL.NSQI.LL...TY..
Retrocopy MNFLQELNNNGSGRL<VDESSENLLNNDLSSSCRFTAVVAPRLPESTLLYLADVLQNSQISLLIYGTYMA

Parental  VGYMRIIIKEHPVIESHPDNAL-EDLRLDKPF-PELREHFQSYDLEHMEKKDHSHTPWIVIVAKYLAQWY
          .G..R.IIKEHPVIE.H.D....EDL.LDKPF..ELREHFQSY.L....K.....T..IVI.AKYLA.W.
Retrocopy FGDRRNIIKEHPVIEFHQDKTK<EDLQLDKPF<SELREHFQSYSLDYTGKDKTIATL*IVIIAKYLA*WN

Parental  SETNGRIPKTYKEKEDFRDLIRQGILKNENGAPEDEENFEEAIKNVNTALNTTQIPSSIEDI-FNDDRCI
          S.TNG..PK....KEDFRDLIR.GILKNE..APEDEENFEEAIKN.NTA.NT.QIP..I.DI.FN...CI
Retrocopy SDTNG*TPKMCQGKEDFRDLIRPGILKNEMRAPEDEENFEEAIKNINTAINTAQIPINIKDI<FNENCCI

Parental  NITKQTPSFWILARALKEFVAKEGQ
          NI..QTP.F..LA.ALK.FV.KE.Q
Retrocopy NISQQTPFF*LLAYALKDFVDKEAQ

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	4.19 RPM
SRP021940_cerebellum	0.00 RPM	7.43 RPM
SRP021940_embryo	0.00 RPM	15.34 RPM
SRP021940_placental_villous	0.00 RPM	9.38 RPM
SRP021940_synovial_membrane	0.00 RPM	4.78 RPM
SRP021940_testis	0.00 RPM	10.04 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_942 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_942 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_942 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000021954	1 retrocopy	retro_ecab_942 ,
Nomascus leucogenys	ENSNLEG00000004047	1 retrocopy	retro_nleu_395,
Otolemur garnettii	ENSOGAG00000014645	1 retrocopy	retro_ogar_1443,
Pongo abelii	ENSPPYG00000007428	2 retrocopies	retro_pabe_3596, retro_pabe_759,