RetrogeneDB ID: retro_nleu_2408

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397353.1:284523..284877(+)
• Located in intron of: ENSNLEG00000013272

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000012979
• Aliases: None
• Description: None

Sequence

>retro_nleu_2408
TACACTCTGGAAATGATTAAACTAGTATCACATAATGAAAGTGCCTGCAACTATTTGAAAGGAATTTTGCAGGATTGTGG
TCTTTCCAAATATCCTAATCTGTTAAGTCAATTACTTGATTTACAACCGAGTCATAGTTCCTCCTATCTAATTGCCTTTC
TTGTGGATATCTATGAAGACATGCTAGAAAACCAGTGTGACAAAAAGGAAGACATTCTTAATAAAGCATTACAGTTATGT
GAGATCCTAGCTCAAGAAAAGGACACTATAAGAAAGGAATATTGGAGATAGATTGGAAGATCCCTTCAAAGCAAACACAG
CACAGAAAATGACTCATCAACAAACGTACAGCAA

Alignment

ORF - retro_nleu_2408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.53 %
• Parental protein coverage: 56.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YTLEMIKLVPHNESAWNYLKGILQDRGLSKYPNLLNQLLDLQPSHSSPYLIAFLVDIYEDMLENQCDNKE
          YTLEMIKLV.HNESA.NYLKGILQD.GLSKYPNLL.QLLDLQPSHSS.YLIAFLVDIYEDMLENQCD.KE
Retrocopy YTLEMIKLVSHNESACNYLKGILQDCGLSKYPNLLSQLLDLQPSHSSSYLIAFLVDIYEDMLENQCDKKE

Parental  DILNKALELCEILAKEKDTIRKEYWRYIGRSLQSKHSTENDSPTNVQQ
          DILNKAL.LCEILA.EKDTIRKEYWR.IGRSLQSKHSTENDS.TNVQQ
Retrocopy DILNKALQLCEILAQEKDTIRKEYWR*IGRSLQSKHSTENDSSTNVQQ

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_2408 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003201	2 retrocopies	retro_btau_1431, retro_btau_1768,
Canis familiaris	ENSCAFG00000005385	1 retrocopy	retro_cfam_941,
Erinaceus europaeus	ENSEEUG00000008272	1 retrocopy	retro_eeur_532,
Homo sapiens	ENSG00000168522	1 retrocopy	retro_hsap_805,
Loxodonta africana	ENSLAFG00000000631	1 retrocopy	retro_lafr_506,
Macaca mulatta	ENSMMUG00000017158	1 retrocopy	retro_mmul_1078,
Monodelphis domestica	ENSMODG00000010003	1 retrocopy	retro_mdom_1656,
Nomascus leucogenys	ENSNLEG00000012979	1 retrocopy	retro_nleu_2408 ,
Pteropus vampyrus	ENSPVAG00000013502	2 retrocopies	retro_pvam_1157, retro_pvam_1433,
Sorex araneus	ENSSARG00000009660	1 retrocopy	retro_sara_109,
Ictidomys tridecemlineatus	ENSSTOG00000011626	1 retrocopy	retro_itri_1221,
Tursiops truncatus	ENSTTRG00000008870	1 retrocopy	retro_ttru_579,