RetrogeneDB ID: retro_nleu_175

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:32708354..32709471(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSPA8
• Ensembl ID: ENSNLEG00000007419
• Aliases: None
• Description: None

Sequence

>retro_nleu_175
ATGTCCAAGGGACCTGCAGTTGGTATGGATCTTGGCACCACCTACTCTTGTGTGGGTGTTTTCCAGCATGGAAAAGTAGA
GATAATTGCCAATGATCAGGGAAACTGAACCACTCCAAGCTATGTTGCCTTTACGGACACTAAACAGTTCATCGGTGATG
CCGCAAAGAATCAATTTGCAATGAACCCCACCAACATAGTTTTTGATGCCAAACGTCTGACTGGACACAGATTTGATGAT
GCTGTTGTCCAGTCTGATATGAAGCATTGGCCCTTCATGGTGTTGAATGATGCTGGCAGGACCAAGGTCCAAGTAGAATA
CAAGGGAGAGACCAAAAGCTTCTGTCCAGAGGAGGTATCCTCTATGGTTCTGACAAAGATGAAGGAAATTGCAGAAGCTT
ACCTTGGGAAGACTGTTACCAATGCTGTGGTCACAGTGCCAGCTTACTTTAATGATTCTCAGCTTCAGGCTACCAAAGAT
GCTGGAACTATTGCTGGTCTCATTGTACTTAGAATTAATGAGCCAACTGCTGCTGCTATTGCTTACAAGAGCTCAGACAA
AAAGGTTGGAGCAGAAAGAAACGTGCTTATCTTTGACCTGGGAGGTGGCAATTTCGATGTGTCAATCCTCACTATTGAGG
ATGGAATCTGTGAGGTCAAGTATGCAGCCGGAGACACCCACTTGGGTGGAGAAGATTTTGACAACCGAATGGTCAACGGT
TTTATTTGCTGAGTTCAAGTGCAAGCATAAGAAGGACATCAGTGAGAGCAAGAGAGCTGTAAGACGCCTCCGTACTGCTT
GTGAACGTGCTAAGCGTACTCTCTCTTCCAGCAACCAGGCCAGTATTGAGATCGATTCTCTCTATGAAGGAATTGACTTC
TATACCTCCATTACCTGTGCCCAATTTGAAGAATTGAATGCTGACCTGTTCTGTGGCACCCTGGACCCAGCAGAGAAAGC
CCTTCGAGATGCCAAACCAGACAAGTCACAAATTCATGATATTGTCCTGGTTGGCGGTTCCATTAGTATCCCCAAGATTC
AGAAGCTTCTCCAAGATTTCTTCAGTGGAAAATAACTGAATAAGAGCATCAACCCTGATGAAGCTGTTGCTTGTGGC

Alignment

ORF - retro_nleu_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.11 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDA
          MSKGPAVG.DLGTTYSCVGVFQHGKVEIIANDQGN.TTPSYVAFTDT...IGDAAKNQ.AMNPTN.VFDA
Retrocopy MSKGPAVGMDLGTTYSCVGVFQHGKVEIIANDQGN*TTPSYVAFTDTKQFIGDAAKNQFAMNPTNIVFDA

Parental  KRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVT
          KRL.G.RFDDAVVQSDMKHWPFMV.NDAGR.KVQVEYKGETKSF.PEEVSSMVLTKMKEIAEAYLGKTVT
Retrocopy KRLTGHRFDDAVVQSDMKHWPFMVLNDAGRTKVQVEYKGETKSFCPEEVSSMVLTKMKEIAEAYLGKTVT

Parental  NAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAY-GLDKKVGAERNVLIFDLGGGTFDVSI
          NAVVTVPAYFNDSQ.QATKDAGTIAGL.VLR.INEPTAAAIAY...DKKVGAERNVLIFDLGGG.FDVSI
Retrocopy NAVVTVPAYFNDSQLQATKDAGTIAGLIVLR-INEPTAAAIAYKSSDKKVGAERNVLIFDLGGGNFDVSI

Parental  LTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFI-AEFKRKHKKDISENKRAVRRLRTACERAKRTLSSST
          LTIEDGI.EVK..AGDTHLGGEDFDNRMVN.FI.AEFK.KHKKDISE.KRAVRRLRTACERAKRTLSSS.
Retrocopy LTIEDGICEVKYAAGDTHLGGEDFDNRMVNGFI>AEFKCKHKKDISESKRAVRRLRTACERAKRTLSSSN

Parental  QASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQK
          QASIEIDSLYEGIDFYTSIT.A.FEELNADLF.GTLDP.EKALRDAK.DKSQIHDIVLVGGS..IPKIQK
Retrocopy QASIEIDSLYEGIDFYTSITCAQFEELNADLFCGTLDPAEKALRDAKPDKSQIHDIVLVGGSISIPKIQK

Parental  LLQDFFNGKELNKSINPDEAVAYG
          LLQDFF.GK.LNKSINPDEAVA.G
Retrocopy LLQDFFSGK*LNKSINPDEAVACG

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_175 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 23 parental genes, and 51 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004884	2 retrocopies	retro_acar_21, retro_acar_6,
Anas platyrhynchos	ENSAPLG00000010667	1 retrocopy	retro_apla_6,
Canis familiaris	ENSCAFG00000011666	3 retrocopies	retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis	ENSCING00000009665	1 retrocopy	retro_cint_12,
Cavia porcellus	ENSCPOG00000004169	3 retrocopies	retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi	ENSCSAVG00000008588	1 retrocopy	retro_csav_3,
Equus caballus	ENSECAG00000013510	2 retrocopies	retro_ecab_291, retro_ecab_628,
Echinops telfairi	ENSETEG00000010996	1 retrocopy	retro_etel_43,
Ficedula albicollis	ENSFALG00000005812	1 retrocopy	retro_falb_18,
Gallus gallus	ENSGALG00000006512	1 retrocopy	retro_ggal_8,
Loxodonta africana	ENSLAFG00000030312	4 retrocopies	retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo	ENSMGAG00000001929	1 retrocopy	retro_mgal_9,
Myotis lucifugus	ENSMLUG00000004834	3 retrocopies	retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica	ENSMODG00000012958	2 retrocopies	retro_mdom_127, retro_mdom_99,
Mustela putorius furo	ENSMPUG00000005810	9 retrocopies	retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Nomascus leucogenys	ENSNLEG00000007419	8 retrocopies	retro_nleu_119, retro_nleu_1258, retro_nleu_1261, retro_nleu_1582, retro_nleu_175 , retro_nleu_1781, retro_nleu_370, retro_nleu_64,
Nomascus leucogenys	ENSNLEG00000017348	1 retrocopy	retro_nleu_751,
Oreochromis niloticus	ENSONIG00000004759	1 retrocopy	retro_onil_2,
Pelodiscus sinensis	ENSPSIG00000012450	2 retrocopies	retro_psin_17, retro_psin_5,
Ictidomys tridecemlineatus	ENSSTOG00000003756	1 retrocopy	retro_itri_51,
Taeniopygia guttata	ENSTGUG00000000491	1 retrocopy	retro_tgut_7,
Takifugu rubripes	ENSTRUG00000005265	1 retrocopy	retro_trub_30,
Xiphophorus maculatus	ENSXMAG00000001602	1 retrocopy	retro_xmac_20,