RetrogeneDB ID: retro_nleu_2857

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397453.1:670635..671939(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CASC4
• Ensembl ID: ENSNLEG00000005533
• Aliases: None
• Description: cancer susceptibility candidate 4 [Source:HGNC Symbol;Acc:24892]

Sequence

>retro_nleu_2857
ATGGTGGGTTTCGGGGCCAACCGGCCGGCTGGCCGCCTGCCTTCTCTCGTGCTGGTGGTGCTGCTGGTAGTGACCGTCGT
CCTCACCTTCAACTGCTGGAGCATCTCTTCCTGCCACGTCCTGCTTCAGGAGGAGGTGGCCGAGCTGCAGGGCCAGGTCC
AGCGCATCGAAGTGGCCCGCGAGCGGCTGGAAAAGCGCAGTTCGGACCTCTTGCTGTTGGTGGACAAGCACAAGAAACAT
CACCAGAAGGAGGCTGACTACGGCCGCCTCAACAGCCGGCTGCAGGTCAGAGAGGGCCTGGGGAAGAGATGCGAGGATGA
CAAAGTTAAACTACAGAAAAACATATCATTATCAGATGGCAGACATACATCATTTAAAGGAGCACCTTGCCGAGCTTCGT
CAGGAGTTTCTTCGACAAGAAGACCAGCTTCAGGACTATAGGAAGAACAATACTTACCTTGTGAAGAGGTTAGAATATGA
AAGTTTTCAGTGTGGACAGCAGATCAAGGAATTGAGAGCACAGTATGAAGAAAATATTAAAAAGTTAGCAGACCAGTTTT
TACAGTAACAAAAGGAAGAGGCCCTCAAGATTCAATCAAATGACGGAAAAGAACTGGGTGTAAACGATCAAGTAGTACCT
AAAAATATTCCAAAAGTAGCTGAGAATGTTGCAGATAAGAATGAAGAACCCTCAAGCAATCATATTCTACATGGGAAAGA
ACAAATCAAGAGGTGGTGATGCAGGGATGCCTGGAATAGAAAAGAATGACCTAGCAAAAGTTGATGATCTTCCCCCTGCT
TTAAGGAAGGCTCCTATTTCAGTTTCTCAACATGAAATTCATCAAGCCATCTCCCATCTTCCAACTGGACAACCTCTCTC
CCCAGGTATGCCTCCAGATTCACACGTAAACCACAATGGAAACCCTGGTACTTCAAAACAGAAGCCTTCCGGTCCTCTTC
AGCATTTAATTCCAGGCTCAAACTTGGACAGTGAACCTAGAATTCAAACAGATATACTAAAGCAGGCTTCCAAGGATAGA
GTCAGTGAGTTACATAAATTGAAGCAAAGCCAATTCTTTGATGAGAATGAATCCCCTCTTGATCTGCAGCATGGCTCTAA
ACTGGCGGATTATAATGGGGATGATGGTAACGTAGGTGAGTATGAGGTAGACAAGCAGGCTGAGCTGGATTACAATGAGG
AAGAAGATGATGATGGTGGAGCGAAAGATGTCCAAGATGATGAAGAACGAGAGCTTCAAATGGATCCTGCAGACTATGGA
AAGCAACATTTCAATGATGTCCTT

Alignment

ORF - retro_nleu_2857 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVGFGANRRAGRLPSLVLVVLLVVIVVLAFNYWSISSRHVLLQEEVAELQGQVQRTEVARGRLEKRNSDL
          MVGFGANR.AGRLPSLVLVVLLVV.VVL.FN.WSISS.HVLLQEEVAELQGQVQR.EVAR.RLEKR.SDL
Retrocopy MVGFGANRPAGRLPSLVLVVLLVVTVVLTFNCWSISSCHVLLQEEVAELQGQVQRIEVARERLEKRSSDL

Parental  LLLVDTHKKQIDQKEADYGRLSSRLQAREGLGKRCEDDKVKLQNNIS-YQMADIHHLKEQLAELRQEFLR
          LLLVD.HKK...QKEADYGRL.SRLQ.REGLGKRCEDDKVKLQ.NIS.YQMADIHHLKE.LAELRQEFLR
Retrocopy LLLVDKHKKH-HQKEADYGRLNSRLQVREGLGKRCEDDKVKLQKNIS>YQMADIHHLKEHLAELRQEFLR

Parental  QEDQLQDYRKNNTYLVKRLEYESFQCGQQIKELRAQHEENIKKLADQFLQEQKQEAHKIQSNDGKELDIN
          QEDQLQDYRKNNTYLVKRLEYESFQCGQQIKELRAQ.EENIKKLADQFLQ.QK.EA.KIQSNDGKEL..N
Retrocopy QEDQLQDYRKNNTYLVKRLEYESFQCGQQIKELRAQYEENIKKLADQFLQ*QKEEALKIQSNDGKELGVN

Parental  DQVVPKNIPKIAENVADKNEEPSSNHIPH-GKEQIKRGGDAGMPGIEENDLAKVDDLPPALRKPPISVSQ
          DQVVPKNIPK.AENVADKNEEPSSNHI.H.GK....RGGDAGMPGIE.NDLAKVDDLPPALRK.PISVSQ
Retrocopy DQVVPKNIPKVAENVADKNEEPSSNHILH>GKNK-SRGGDAGMPGIEKNDLAKVDDLPPALRKAPISVSQ

Parental  HESHQAISHLPTGQPLSPNMPPDSHVNHHGNPGTSKQNPSSPLQRLIPGSNLDSEPRIQTDILKQATKDR
          HE.HQAISHLPTGQPLSP.MPPDSHVNH.GNPGTSKQ.PS.PLQ.LIPGSNLDSEPRIQTDILKQA.KDR
Retrocopy HEIHQAISHLPTGQPLSPGMPPDSHVNHNGNPGTSKQKPSGPLQHLIPGSNLDSEPRIQTDILKQASKDR

Parental  VSDFHKLKQSRFFDENESPVDPQHGSKLADYNGDDGNVGEYEADKQAELAYNEEEDGDGGEEDVQDDEER
          VS..HKLKQS.FFDENESP.D.QHGSKLADYNGDDGNVGEYE.DKQAEL.YNEEED.DGG..DVQDDEER
Retrocopy VSELHKLKQSQFFDENESPLDLQHGSKLADYNGDDGNVGEYEVDKQAELDYNEEEDDDGGAKDVQDDEER

Parental  ELQMDPADYGKQHFNDVL
          ELQMDPADYGKQHFNDVL
Retrocopy ELQMDPADYGKQHFNDVL

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_2857 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006998	4 retrocopies	retro_chof_1422, retro_chof_1445, retro_chof_2453, retro_chof_627,
Homo sapiens	ENSG00000166734	1 retrocopy	retro_hsap_1238,
Nomascus leucogenys	ENSNLEG00000005533	1 retrocopy	retro_nleu_2857 ,
Oryctolagus cuniculus	ENSOCUG00000005362	1 retrocopy	retro_ocun_1472,
Pongo abelii	ENSPPYG00000006428	1 retrocopy	retro_pabe_1083,
Pan troglodytes	ENSPTRG00000007010	1 retrocopy	retro_ptro_852,