RetrogeneDB ID: retro_nleu_700

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397270.1:44454398..44455303(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMMECR1L
• Ensembl ID: ENSNLEG00000015793
• Aliases: None
• Description: None

Sequence

>retro_nleu_700
CCTCCAGTGGAGCCCAAGTTGGCAGCAGGCTGTTGGGGGAGCAAGAAGCCCAAATTATCTGGAAGTGAAACATACAGTCA
TGAGAACGAGTCCACAGCCTTCCCTGGCCCTAGGTCAGGACCTCTTCAAAATTGCCAGCATGTCGACAGCAGCAGCAGAT
AGGAGAGTGTGTTGGACTTAACTGTGGGACCTGGAAGCTCTCGCATCACATGAACGAATCCAGCATCAGGAGCACTGAGC
CCTCTCCCCGAGTCTAATGGAATGGCAGCTCCACAAAGAATCTGGAGGTGACTGCACAGATGTGCTGCTACTGCTTTACT
GAACTCTACTGTCAGCTCTATGGCTTTCCACAGCCACAACTTCCTAGATTCACCAATGACCCCTGTCCGCTCTTTGTGAC
ATGGAAGACAGGGAGGGACAAGTGGCTTTATGGCTGCCTTGGGACCTTCTCAGCCATGAATCTTTATTCAGGACTCAGGG
AATGCATGTTAGCCATTGCATTTAAGGACAGCTGATTTCCCCTCCATTCTGAGAGGAGCTGCCTAAGCTTTTCTGCTCTG
TCTCCCTCCATACTAACCTTGAGGATGCTAGTGATTACCTGGACTGGGAGATAGGGGTCCATGGGATTTAAATTGAATTC
ATTAATGAAAAAGGCATCAAACGTACAGCCTCATTTTCACCTGAGGTTGCTAAGGAACAAAACTGGAGTCAGATCCAAAC
AATAGAGTCCTTGCTCAGGAAAGGTAGCTTTAAGGATCAATTACCAGCGAATTTGGAAAAATGGTCAAACTCACCAGGTA
CTAAAGTGAGAAGGTGACAATCAGTTTTGCAGAGTATATTGCTTCTTGACAGCACTGTTTCCAGAACCATACCCTCCATG
CCCCACCCCCTACAATCATTACTCC

Alignment

ORF - retro_nleu_700 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.55 %
• Parental protein coverage: 97.74 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PPLEPKLAAGCCGVKKPKLSGSGTHSHGNQSTTVPGSSSGPLQNHQHVDSSSGRENVSDLTLGPGNSPIT
          PP.EPKLAAGC.G.KKPKLSGS.T.SH.N.ST..PG..SGPLQN.QHVDSSS..E.V.DLT.GPG.S.IT
Retrocopy PPVEPKLAAGCWGSKKPKLSGSETYSHENESTAFPGPRSGPLQNCQHVDSSSR*ESVLDLTVGPGSSRIT

Parental  RMNPASGALSPLPRPNGTA-NTTKNLVVTAEMCCYCFDVLYCHLYGFPQPRLPRFTNDPYPLFVTWKTGR
          ..NPASGALSPLP..NG.A...TKNL.VTA.MCCYCF..LYC.LYGFPQP.LPRFTNDP.PLFVTWKTGR
Retrocopy *TNPASGALSPLPESNGMA<SSTKNLEVTAQMCCYCFTELYCQLYGFPQPQLPRFTNDPCPLFVTWKTGR

Parental  DKRLRGCIGTFSAMNLHSGLREYTLTSALKDSRFP-PLTREELPKLFCSVSLLTNFEDASDYLDWEVGVH
          DK.L.GC.GTFSAMNL.SGLRE..L..A.KDS.FP.P...EELPKLFCSVSL.TN.EDASDYLDWE.GVH
Retrocopy DKWLYGCLGTFSAMNLYSGLRECMLAIAFKDS*FP<PPF*EELPKLFCSVSLHTNLEDASDYLDWEIGVH

Parental  GIRIEFINEKGVKRTATYLPEVAKEQDWDQIQTIDSLLRKGGFK-APITSEFRKTIKLTRYRSEKVTISY
          GI.IEFINEKG.KRTA...PEVAKEQ.W.QIQTI.SLLRKG.FK...ITSEF.K..KLTRY.SEKVTIS.
Retrocopy GI*IEFINEKGIKRTASFSPEVAKEQNWSQIQTIESLLRKGSFK<GSITSEFGKMVKLTRY*SEKVTISF

Parental  AEYIASRQHCFQNGTLHAPP-LYNHYS
          AEYIAS.QHCFQN.TLHAPP..YNHYS
Retrocopy AEYIAS*QHCFQNHTLHAPP<PYNHYS

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_700 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009373	1 retrocopy	retro_chof_1566,
Callithrix jacchus	ENSCJAG00000010743	1 retrocopy	retro_cjac_383,
Equus caballus	ENSECAG00000023095	1 retrocopy	retro_ecab_1085,
Echinops telfairi	ENSETEG00000000510	1 retrocopy	retro_etel_9,
Homo sapiens	ENSG00000144233	1 retrocopy	retro_hsap_1227,
Gorilla gorilla	ENSGGOG00000014448	1 retrocopy	retro_ggor_961,
Myotis lucifugus	ENSMLUG00000006871	1 retrocopy	retro_mluc_684,
Macaca mulatta	ENSMMUG00000001987	1 retrocopy	retro_mmul_1302,
Mus musculus	ENSMUSG00000041915	2 retrocopies	retro_mmus_1330, retro_mmus_352,
Nomascus leucogenys	ENSNLEG00000015793	1 retrocopy	retro_nleu_700 ,
Pan troglodytes	ENSPTRG00000012437	1 retrocopy	retro_ptro_843,
Sarcophilus harrisii	ENSSHAG00000014762	1 retrocopy	retro_shar_86,