RetrogeneDB ID: retro_nleu_1585

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:15765983..15766868(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACTA1
• Ensembl ID: ENSNLEG00000014347
• Aliases: None
• Description: None

Sequence

>retro_nleu_1585
TGGGACGACATGGAGAAGATCTGGCACCACACCTTCTACAACAAGCTGCACGTGGCCCCAGAGGAGTACCTTGTGCTGCT
GACCAAGGCCCCCCCAGAACCCCAAGGCCAACAGAGAGATGACTCAGATCATGTTTGAGATCTTCAACACCCTGGCCATG
TACATGGCCATCCAAGCTGTGCTGTCCCTCTACGCCTCTGGGTGCACCACTGGCATTGCCATGGACTCTGGAGACGGGGT
CGCCCACACGGTACCCATCTATGAGGGCTACGCTCTCCCCCATGCCATCCTGCATCTGGACCTGGCTGGCTGGGACCTGA
CTGACTACTTCATGAAGATCCTCACCGAGTGCAGCTACCGTTTCACCACCATGGCTGAGCAGGAGATCGTGTGTGACATC
AAGGAGAAGCTGTGCAACGTCGCCCTGGACTTCGAGCACAAGATGGCCACCGGCGCATCCTCCTCCTCTCTGGAGAAGAG
CTACAAGGTGCCTGATGGCCAGGTCATCACCATCGGCAACGAGTGGTTCTGGTATCCAGAGGCACTGTTTCAGCCTTCCT
GGGCATGGAATCTTGCGGCATCCAAGAGACCACCTTCAACTCCATCATGAAATGTGACATGGACATCTGCAAAGAACTGT
ATGCCAAAACGGTTCTGTCCAGTGGCACCACCATGTATCTGGGCATTGCTGACAGGATGCAGAAGGAGATCACTGCCCTG
GCACCCAGCTCCATGAAGATCAAGATCATCATGTCCCCAGAGTGCAAGTACTCAGTGTGGATTGGTGGCTCCATCCTGGC
CTCACTGTCCACCTTCCAGCAGATGTGGATTAGCAAGCAGGAGTATGATGAGTTGGGCCCCTCCATCATCCACCACAAAT
GCTTC

Alignment

ORF - retro_nleu_1585 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.19 %
• Parental protein coverage: 78.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  WDDMEKIWHHTFYNELRVAPEEHPTLLTEAP-LNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGR
          WDDMEKIWHHTFYN.L.VAPEE...LLT.AP..NPKANRE.MTQIMFE.FN..AMY.AIQAVLSLYASG.
Retrocopy WDDMEKIWHHTFYNKLHVAPEEYLVLLTKAP>QNPKANRE-MTQIMFEIFNTLAMYMAIQAVLSLYASGC

Parental  TTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLC
          TTGI..DSGDGV.H.VPIYEGYALPHAI..LDLAG.DLTDY.MKILTE..Y.F.T.AE.EIV.DIKEKLC
Retrocopy TTGIAMDSGDGVAHTVPIYEGYALPHAILHLDLAGWDLTDYFMKILTECSYRFTTMAEQEIVCDIKEKLC

Parental  YVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLF-PSFIGMESAGIHETTYNSIMKCDI
          .VALDFE..MAT.ASSSSLEKSY..PDGQVITIGNE.F..PE.LF...F.GMES.GI.ETT.NSIMKCD.
Retrocopy NVALDFEHKMATGASSSSLEKSYKVPDGQVITIGNEWFWYPEALF<SAFLGMESCGIQETTFNSIMKCDM

Parental  DIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWI
          DI.K.LYA..V.S.GTTMY.GIADRMQKEITALAPS.MKIKII..PE.KYSVWIGGSILASLSTFQQMWI
Retrocopy DICKELYAKTVLSSGTTMYLGIADRMQKEITALAPSSMKIKIIMSPECKYSVWIGGSILASLSTFQQMWI

Parental  TKQEYDEAGPSIVHRKCF
          .KQEYDE.GPSI.H.KCF
Retrocopy SKQEYDELGPSIIHHKCF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1585 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000012233	1 retrocopy	retro_nleu_2313,
Nomascus leucogenys	ENSNLEG00000013385	15 retrocopies	retro_nleu_1008, retro_nleu_1058, retro_nleu_1059, retro_nleu_1150, retro_nleu_1347, retro_nleu_1474, retro_nleu_1729, retro_nleu_2193, retro_nleu_2393, retro_nleu_2574, retro_nleu_2669, retro_nleu_3032, retro_nleu_344, retro_nleu_813, retro_nleu_974,
Nomascus leucogenys	ENSNLEG00000014347	1 retrocopy	retro_nleu_1585 ,
Nomascus leucogenys	ENSNLEG00000015157	1 retrocopy	retro_nleu_2751,
Nomascus leucogenys	ENSNLEG00000015506	3 retrocopies	retro_nleu_1525, retro_nleu_1536, retro_nleu_1930,
Ochotona princeps	ENSOPRG00000002854	1 retrocopy	retro_opri_573,
Xenopus tropicalis	ENSXETG00000021417	1 retrocopy	retro_xtro_24,