RetrogeneDB ID: retro_nleu_2305

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397342.1:270194..271617(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPJ
• Ensembl ID: ENSNLEG00000016895
• Aliases: None
• Description: None

Sequence

>retro_nleu_2305
AAATTTGGTGAGTGGCCTCCACTTAAACGACTTACTAGGGAAGCTATGTGAAATTATTTAAAAGAGTAAGGGGATCAAAT
AGTACTTATCCGTCATGCAAAAGTTGTACAGAAGTCATATGGAAATGAAAAAAGGTTTTTTTTGCCCTCCCCCTTGTGTA
TATCTTATGGGCAGTGAATGGAAGAAAATAAAATAACAAATGAAATGCGATGGTTGTTCTGAACAAGAGTCTCAACCCTG
TGCATTTATTGGGATAGGAAATAGTGATCAAGAAATGCAGCAGCTAAACTTGGAAGGAAAGAACTATTGCACAGCCAAAA
CATTGTACATATCTGATTCAGACAAGCAAAGGACTTCATGTTGTCTGTAAAGATGTTCTGTGGCAACGGTGATGACATTG
GTGTGTTCCTCAGCAAGTCATCCAAACCTTCCAAAAAGAAGCAGTCATTGAAAAATGCTGACTTATGCATTGCCTCAGGA
CCAAAGGTGGCTCTGTTTAATCGACTATGATCCCAGACAGTTAGTACCAGATACTTGCACGTAGAAAGAGGTAATTTTCA
TGCTAGTTCACAGCAATGGGGAGCATTTTACATTATTCTTGGATGATGATGAATCAGAAGGAGAAGAATTCACAGTCTGA
GATGGCTACATTCATTATGGACAAACAGCCAAACTTGTGTGCTCAGTTACTGGCATGGCACTCCCAAGACTGATAATTAG
GAAAGTTGATAAGCAGACCACATTATTGGACGCAGATGATCCTGTGTCACAACTCTATAAATGTGCATTTTACCTTGAGG
ACACAGAAAGAAAGTACTTATGCCTTTCTCAAGAAAGAATAATTCCATTTCAGGCCACTCCATGACCAAAAGAACCAAAT
AAAGAGATGATAAATGATGGCGCTTCCTGGGCAATCATTAGCACACATAAGGCAAAGTATACATTTTACAAGAGAACGGG
CCCTGTCCTTGCCATGGTCATGCCTACGCCTGTCGTAGAGAGCCTTAAGTTGAACGGCAGTGGGGACGAAGCAATGCTTG
AACTTACAGGACAGAATTTCACTCCAAATTTATGAGTGTGGTTTGGGGATGTAGAAGCTGAAACTATGTACAGGTGTGGA
GAGAGTATGCTCCGTGTGGTCCCAGACGTTTCTGCATTCTGAGAAGTTTGGAGATAGGTCTGGCAACCCGTCCGGGTTTC
AGTAACTTTGGTCCGAAATGATGGAATCATATATTCCACCAGCCTTACCTTTACCTACACACCAGAAGCAGGGCTGCGGC
CACATTGCAGTGTAGCAGGAGCAATCCTTCAAGCCAGTTCAAGCCACATGCCCCCTAATAACAAATGAAACAGCGAGGGA
AGTTACACAAACGCCAGCACAAATTCAACCAGTGTCACATCATCTACACCAACAGTGGTATCC

Alignment

ORF - retro_nleu_2305 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.44 %
• Parental protein coverage: 83.04 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KFGERPPPKRLTREAMRNYLKERGDQTVLILHAKVAQKSYGNEKRFFCP-PPCVYLMGSGWKKKKEQMER
          KFGE.PP.KRLTREAM.NYLKE.GDQ.VLI.HAKV.QKSYGNEKR...P.PPCVYLMGS.WKK.K.QM..
Retrocopy KFGEWPPLKRLTREAM*NYLKE*GDQIVLIRHAKVVQKSYGNEKRXXXP>PPCVYLMGSEWKKIK*QMKC

Parental  DGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKR-KHFMLSVKMFYGNSDDIGVFLS
          DGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDK..K.FMLSVKMF.GN.DDIGVFLS
Retrocopy DGCSEQESQPCAFIGIGNSDQEMQQLNLEGKNYCTAKTLYISDSDKQ<KDFMLSVKMFCGNGDDIGVFLS

Parental  KRIKVISKPSKKKQSLKNADLCIASGTKVALFNRLRSQTVSTRYLHVEGGNFHASSQQW-GAFFIHLLDD
          K.....SKPSKKKQSLKNADLCIASG.KVALFNRL.SQTVSTRYLHVE.GNFH..S.Q..G..F...LDD
Retrocopy KS----SKPSKKKQSLKNADLCIASGPKVALFNRL*SQTVSTRYLHVERGNFH-ASSQQ>GEHFTLFLDD

Parental  DESEGEEFTVRDGYIHYGQTVKLVCSVTGMALPRLIIRKVDKQTALLDADDPVSQLHKCAFYLKDTERMY
          DESEGEEFTV.DGYIHYGQT.KLVCSVTGMALPRLIIRKVDKQT.LLDADDPVSQL.KCAFYL.DTER.Y
Retrocopy DESEGEEFTV*DGYIHYGQTAKLVCSVTGMALPRLIIRKVDKQTTLLDADDPVSQLYKCAFYLEDTERKY

Parental  LCLSQERIIQFQATPCPKEPNKEMINDGASWTIISTDKAEYTFYEGMGPVLAPVTPVPVVESLQLNGGGD
          LCLSQERII.FQATP.PKEPNKEMINDGASW.IIST.KA.YTFY...GPVLA.V.P.PVVESL.LNG.GD
Retrocopy LCLSQERIIPFQATP*PKEPNKEMINDGASWAIISTHKAKYTFYKRTGPVLAMVMPTPVVESLKLNGSGD

Parental  VAMLELTGQNFTPNLRVWFGPVEAETMYRCGESMLCVVPDISAFREGWRWVRQPVQVPVTLVRNDGIIYS
          .AMLELTGQNFTPNL.VWFG.VEAETMYRCGESML.VVPD.SAF.E.WR.V.QPV.V.VTLVRNDGIIYS
Retrocopy EAMLELTGQNFTPNL*VWFGDVEAETMYRCGESMLRVVPDVSAF*EVWR*VWQPVRVSVTLVRNDGIIYS

Parental  TSLTFTYTPEPGPRPHCSAAGAILRASSSQVPPNESNTNSEGSYTNASTNSTSVTSSTATVVS
          TSLTFTYTPE.G.RPHCS.AGAIL.ASSS..PPN....NSEGSYTNASTNSTSVTSST.TVVS
Retrocopy TSLTFTYTPEAGLRPHCSVAGAILQASSSHMPPN-NK*NSEGSYTNASTNSTSVTSSTPTVVS

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_2305 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003602	1 retrocopy	retro_btau_1507,
Choloepus hoffmanni	ENSCHOG00000001582	4 retrocopies	retro_chof_1172, retro_chof_1278, retro_chof_2449, retro_chof_371,
Homo sapiens	ENSG00000168214	6 retrocopies	retro_hsap_4169, retro_hsap_4171, retro_hsap_4173, retro_hsap_4174, retro_hsap_4256, retro_hsap_4316,
Gorilla gorilla	ENSGGOG00000004582	1 retrocopy	retro_ggor_2853,
Mus musculus	ENSMUSG00000039191	2 retrocopies	retro_mmus_2348, retro_mmus_2819,
Nomascus leucogenys	ENSNLEG00000016895	1 retrocopy	retro_nleu_2305 ,
Oryctolagus cuniculus	ENSOCUG00000013449	1 retrocopy	retro_ocun_1445,
Pan troglodytes	ENSPTRG00000015968	1 retrocopy	retro_ptro_2829,
Tursiops truncatus	ENSTTRG00000009022	2 retrocopies	retro_ttru_1151, retro_ttru_1593,