RetrogeneDB ID: retro_nleu_1997

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397321.1:5398708..5400211(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HK2
• Ensembl ID: ENSNLEG00000001062
• Aliases: None
• Description: None

Sequence

>retro_nleu_1997
ATGATTGCCTCGCATTTGCTTGCCTACTTCTTCACGGAGCTCAACCATGACCAAGTGCAGAAGGTTGACCACTATCTCTA
CCACATGCGCCTCTCTGATGAGACCCTCTTGGAGATCTCTAAGAGGTTCCACAAGGAGATAGAGAAAGGGCTCGGAGCCA
CCACTCGCCCCACTGCAGCAGTGAAGATGCTGCCCACCTTTGTGAGGTCCACTCCAGATGGGACAGAACATGGAGAGTTC
CTGGCTCTGGACCTTGGAGGGACCAATTTCCATGTGCTTTGGGTGAAAGTAACGGACAATGGGCTCCAGAAGGTGGAGAT
GGAGAACCAGATCTATGCCATCCCCGAGGATGTCATGCGAGGCAGTGACACCCAGCTGTTTGACCACATTGCCGAATGCC
TGGATAACTTCATGGATAAGCTACAAATCAAAGACAAGAAGCTGCCATTGGGTTTTACCTTCTCGTTCCCCTGCCACCAG
ACTAAACTAGATGAGAGTTTCCTGGTCTCATGGACCAAGAGATTCAAGTCCAGTGGAGTGGAAGGCAGAGACGTTGTGCC
TCTGATCCGGAAGTCCATCCAGAGGAGAGGGGACTTTGATATCGACATTGTGGCTGTGGTGAATGACACAGTTGGGACCA
TGACGACCTGTGGTTATGATGACCACAACTGTGAGATTGGTTTCATTGTGGGCACGGACAGCAATGCCTGCTACATGGAA
GAGACGCACCAAATCGACATTGTGGAAGGTGACGAGGGGCAGATGTGTATCGATATGGAGTGGGGGGCCTTCGGGGACGA
TGGCTCGCTCAATGACATTCGCACTGAGTTTGACCAGGAGATTGACATGGGCTCACTGAACCTGGGGAAGCAACTGTTTG
AGAAGATGATCAGTGGGATGTACATGGGGGAGCTGGTGAGGTTTATCCTGGTGAAGATGGCCAAGGAGGAACTGCTCTTT
GGGGGGAAGCTCAGCCCAGAGCTTCTCAACACTGGTCGCTTTGAGACCAAAGACATCTCAGACATTGAAGGGGAGAAGGA
TGGCATCCGGAAGGCCCATGAGGTCCTGATGCGGTTGGGCATGGACCCGACTCAGGAGGACTGCGTGACCACTCACCGGA
TCTGCCAGATCGTGTCCACACACTCCGCCAGCCTGTGCACAGCCACCCTGGCAGCCGAGCTGCAGCACATCAAGGAAAAC
AAAGGCGAGGAGCAGCTGCGCCCTACTATTGGGGTCGACGGCTCCGTCTACAAGAAACACCCCCATTTTGCCAAGCATCT
ACATAAGACCGTGTGGCGGCTGGTGCCTGAATGCTATGTCCGCTTCCTCCGCTCCGAGGATGGCAGTGGCAAAGATGCAG
CCATGGTGACAGCAGTGGCTTACCGGCTGGCCGATCAACACCGTGCCCGCCAGAAGACACTAGAGCCTCTGCAGCTGAAC
CATGACCAGCTGTTGGAGGTCAAGAGGAGGATGAAGGTAGAAATGGAGCGAGGTCTGAGCAAG

Alignment

ORF - retro_nleu_1997 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.02 %
• Parental protein coverage: 54.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIASHLLAYFFTELNHDQVQKVDQYLYHMRLSDETLLEISKRFRKEMEKGLGATTHPTAAVKMLPTFVRS
          MIASHLLAYFFTELNHDQVQKVD.YLYHMRLSDETLLEISKRF.KE.EKGLGATT.PTAAVKMLPTFVRS
Retrocopy MIASHLLAYFFTELNHDQVQKVDHYLYHMRLSDETLLEISKRFHKEIEKGLGATTRPTAAVKMLPTFVRS

Parental  TPDGTEHGEFLALDLGGTNFRVLWVKVTDNGLQKVEMENQIYAIPEDIMRGSGTQLFDHIAECLANFMDK
          TPDGTEHGEFLALDLGGTNF.VLWVKVTDNGLQKVEMENQIYAIPED.MRGS.TQLFDHIAECL.NFMDK
Retrocopy TPDGTEHGEFLALDLGGTNFHVLWVKVTDNGLQKVEMENQIYAIPEDVMRGSDTQLFDHIAECLDNFMDK

Parental  LQIKDKKLPLGFTFSFPCHQTKLDESFLVSWTKGFKSSGVEGRDVVTLIRKAIQRRGDFDIDIVAVVNDT
          LQIKDKKLPLGFTFSFPCHQTKLDESFLVSWTK.FKSSGVEGRDVV.LIRK.IQRRGDFDIDIVAVVNDT
Retrocopy LQIKDKKLPLGFTFSFPCHQTKLDESFLVSWTKRFKSSGVEGRDVVPLIRKSIQRRGDFDIDIVAVVNDT

Parental  VGTMMTCGYDDHNCEIGLIVGTGSNACYMEEMRHIDMVEGDEGRMCINMEWGAFGDDGSLNDIRTEFDQE
          VGTM.TCGYDDHNCEIG.IVGT.SNACYMEE...ID.VEGDEG.MCI.MEWGAFGDDGSLNDIRTEFDQE
Retrocopy VGTMTTCGYDDHNCEIGFIVGTDSNACYMEETHQIDIVEGDEGQMCIDMEWGAFGDDGSLNDIRTEFDQE

Parental  IDMGSLNPGKQLFEKMISGMYMGELVRLILVKMAKEELLFGGKLSPELLNTGRFETKDISDIEGEKDGIR
          IDMGSLN.GKQLFEKMISGMYMGELVR.ILVKMAKEELLFGGKLSPELLNTGRFETKDISDIEGEKDGIR
Retrocopy IDMGSLNLGKQLFEKMISGMYMGELVRFILVKMAKEELLFGGKLSPELLNTGRFETKDISDIEGEKDGIR

Parental  KAREVLMRLGLDPTQEDCVATHRICQIVSTRSASLCAATLAAVLQRIKENKGEERLRSTVGVDGSVYKKH
          KA.EVLMRLG.DPTQEDCV.THRICQIVST.SASLC.ATLAA.LQ.IKENKGEE.LR.T.GVDGSVYKKH
Retrocopy KAHEVLMRLGMDPTQEDCVTTHRICQIVSTHSASLCTATLAAELQHIKENKGEEQLRPTIGVDGSVYKKH

Parental  PHFAKRLHKTVRRLVPDCDVRFLRSEDGSGKGAAMVTAVAYRLADQHRARQKTLEPLQLSHDQLLEVKRR
          PHFAK.LHKTV.RLVP.C.VRFLRSEDGSGK.AAMVTAVAYRLADQHRARQKTLEPLQL.HDQLLEVKRR
Retrocopy PHFAKHLHKTVWRLVPECYVRFLRSEDGSGKDAAMVTAVAYRLADQHRARQKTLEPLQLNHDQLLEVKRR

Parental  MKIEMERGLCK
          MK.EMERGL.K
Retrocopy MKVEMERGLSK

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_1997 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000159399	1 retrocopy	retro_hsap_4864,
Nomascus leucogenys	ENSNLEG00000001062	1 retrocopy	retro_nleu_1997 ,
Pongo abelii	ENSPPYG00000012260	1 retrocopy	retro_pabe_3781,
Pan troglodytes	ENSPTRG00000012104	1 retrocopy	retro_ptro_3239,