RetrogeneDB ID: retro_nleu_1129

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:237264..238222(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3I
• Ensembl ID: ENSNLEG00000002426
• Aliases: None
• Description: None

Sequence

>retro_nleu_1129
AAGCTGGTCCTACTGTAGGGCCATGAGTGGTTCATTAGGCAGATGAAGTATAGCTGTGAAGGAGACCTCCTCTTCACCGT
GGCCAAGGAACCTATCATTAATGCATGGTACTCTGTGAATGGTGAGAGGCTGGGCATCTACGTGGGCCATACCAGAGCTG
TGTGGTATGTGGATGCTGACTGGGACACCAAGCAAGTCCTCACCCGTTCAGCTGACAACGATCTTTCAGCCTGTGAAACA
GGGAAACAGCTGGCCCTACTCAAGACCAATTCAACTGTGTGGATCTTCAGTTTTGACTTTGGGGGCAATATCATCACGTT
CTCCACGGAGAAGAAGAAAAGCTGTCAGTGCTTTGTGAGCTTATTTGACCTGCAGGATCTGAGCCAGATTGACAGCAATG
AGTGCTACCTGAAGATCCCTTGCAATGACTCTAAAATCACTAGTGCCGTTTGGGGCTCCTGTGGGGAGTGCATCATTGCA
GGCCATGAGAGTGGAAAGCTAAACCAGTATCGTGCCAAGTCTGGAGAGATGTTGGTGAAGGTTAAGGAGCACTCCCAGCA
GATTAATGACATCCAGTTATCCAGGGACATGACCGTGTTTGTCACTGCATCCAAAGACAACACAGCCAAGCTTTTTGACT
CTACAACTCTTCAACATCAGAAGACTTTCTGAACAGAAAGCCCCATCAGCTCAGCTACCCTCTCCCCCAACAATGACCAT
ATTGTGCTGGGCGGTGGTCAGGAAGCCATGGATGTAACCACAACGTTCACCAGGATTGGCAAGTTTGAGTCTGGGTTCCT
CCATTCGGCCTTTGAAGAAGAGTTCAGAAGAGTCAAGGGGCACTTTGGACCTATCAACAGTGTTGCCTTCCATCCTGATG
GCAAGAGCTACAGCAGCGGCAGTGGCAATGAGGATGGTTACATCCATAACCTACTACTTCGACCCACAGTACTTTGAA

Alignment

ORF - retro_nleu_1129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.95 %
• Parental protein coverage: 98.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KPILLQGHERSITQIKYNREGDLLFTVAKDPIVNVWYSVNGERLGTYMGHTGAVWCVDADWDTKHVLTGS
          K..LL.GHE..I.Q.KY..EGDLLFTVAK.PI.N.WYSVNGERLG.Y.GHT.AVW.VDADWDTK.VLT.S
Retrocopy KLVLL*GHEWFIRQMKYSCEGDLLFTVAKEPIINAWYSVNGERLGIYVGHTRAVWYVDADWDTKQVLTRS

Parental  ADNSCRLWDCETGKQLALLKTNSAVRTCGFDFGGNIIMFSTDKQMGYQCFVSFFDLRDPSQIDNNEPYMK
          ADN...L..CETGKQLALLKTNS.V....FDFGGNII.FST.K....QCFVS.FDL.D.SQID.NE.Y.K
Retrocopy ADND--LSACETGKQLALLKTNSTVWIFSFDFGGNIITFSTEKKKSCQCFVSLFDLQDLSQIDSNECYLK

Parental  IPCNDSKITSAVWGPLGECIIAGHESGELNQYSAKSGEVLANVKEHSRQINDIQLSRDMTMFVTASKDNT
          IPCNDSKITSAVWG..GECIIAGHESG.LNQY.AKSGE.L..VKEHS.QINDIQLSRDMT.FVTASKDNT
Retrocopy IPCNDSKITSAVWGSCGECIIAGHESGKLNQYRAKSGEMLVKVKEHSQQINDIQLSRDMTVFVTASKDNT

Parental  AKLFDSTTLEHQKTFRTERPVNSAALSPNYDHVVLGGGQEAMDVTTTSTRIGKFEARFFHLAFEEEFGRV
          AKLFDSTTL.HQKTF.TE.P..SA.LSPN.DH.VLGGGQEAMDVTTT.TRIGKFE..F.H.AFEEEF.RV
Retrocopy AKLFDSTTLQHQKTF*TESPISSATLSPNNDHIVLGGGQEAMDVTTTFTRIGKFESGFLHSAFEEEFRRV

Parental  KGHFGPINSVAFHPDGKSYSSG--GEDGYVR-IHYFDPQYFE
          KGHFGPINSVAFHPDGKSYSSG...EDGY.....YFDPQYFE
Retrocopy KGHFGPINSVAFHPDGKSYSSGSGNEDGYIH>TYYFDPQYFE

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_1129 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 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010674	1 retrocopy	retro_cfam_321,
Callithrix jacchus	ENSCJAG00000006810	1 retrocopy	retro_cjac_3104,
Echinops telfairi	ENSETEG00000008047	1 retrocopy	retro_etel_1497,
Homo sapiens	ENSG00000084623	2 retrocopies	retro_hsap_3888, retro_hsap_3894,
Gorilla gorilla	ENSGGOG00000001579	3 retrocopies	retro_ggor_2540, retro_ggor_2615, retro_ggor_2623,
Loxodonta africana	ENSLAFG00000017026	1 retrocopy	retro_lafr_1073,
Macaca mulatta	ENSMMUG00000006119	2 retrocopies	retro_mmul_1730, retro_mmul_1733,
Monodelphis domestica	ENSMODG00000017481	2 retrocopies	retro_mdom_1054, retro_mdom_822,
Nomascus leucogenys	ENSNLEG00000002426	2 retrocopies	retro_nleu_1129 , retro_nleu_1135,
Nomascus leucogenys	ENSNLEG00000004160	2 retrocopies	retro_nleu_1301, retro_nleu_1970,
Pongo abelii	ENSPPYG00000001598	2 retrocopies	retro_pabe_3169, retro_pabe_3175,