RetrogeneDB ID: retro_nleu_178

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397261.1:38655389..38655732(+)
• Located in intron of: ENSNLEG00000016377

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000241343
• Ensembl ID: ENSNLEG00000007540
• Aliases: None
• Description: None

Sequence

>retro_nleu_178
AGATTTGAGTCTTTCCATGCCAATAGCACTCCCACAAACGTGGTGAACATTCCTAAAACCCACCAAATTTTCTGTGAGAA
GTGTGGCAAGCACCAACCCCACAAAGTGACACAGGGCAAGAAGGGCAAGGATTCTCTGTATGCCCAGGGAAAGTGGTGTT
ATGACAGATAGCAGGGTGGCTCTGGTGGGCAGACTAAGCCAATTATCCAGAAAAAAGCTAAAACTACAAAGAAGATTGTG
CTAAGGCTTAGTGCATTAAGCCCAGCCCAACTGCAGATCTAAGAGAATGCTAGCTATCAAAAGATGCAAGCATTTTGAAC
TGGAAGGAGATAAGAAGAGACGG

Alignment

ORF - retro_nleu_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.09 %
• Parental protein coverage: 76.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QFLSFRADNAHASMVNVPKTRRTFCKKCGKHQPHKVTQYKKGKDSLYAQGKRRYDRKQSGYGGQTKPIF-
          .F.SF.A.......VN.PKT...FC.KCGKHQPHKVTQ.KKGKDSLYAQGK..YDR.Q.G.GGQTKPI..
Retrocopy RFESFHANSTPTNVVNIPKTHQIFCEKCGKHQPHKVTQGKKGKDSLYAQGKWCYDR*QGGSGGQTKPII>

Parental  RKKAKTTKKIVLRL-ECVEPNCRSKRMLAIKRCKHFELGGDKKRK
          RKK.K........L.....PNCRSKRMLAIKRCKHFEL.GDKKR.
Retrocopy RKKLKLQRRLC*GLVH*AQPNCRSKRMLAIKRCKHFELEGDKKRR

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_178 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 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008503	1 retrocopy	retro_acar_98,
Ailuropoda melanoleuca	ENSAMEG00000009384	1 retrocopy	retro_amel_85,
Callithrix jacchus	ENSCJAG00000004864	4 retrocopies	retro_cjac_304, retro_cjac_353, retro_cjac_55, retro_cjac_72,
Equus caballus	ENSECAG00000015464	9 retrocopies	retro_ecab_129, retro_ecab_131, retro_ecab_204, retro_ecab_219, retro_ecab_265, retro_ecab_268, retro_ecab_294, retro_ecab_543, retro_ecab_646,
Homo sapiens	ENSG00000257529	1 retrocopy	retro_hsap_1353,
Monodelphis domestica	ENSMODG00000025578	2 retrocopies	retro_mdom_1878, retro_mdom_971,
Nomascus leucogenys	ENSNLEG00000007540	27 retrocopies	retro_nleu_1003, retro_nleu_1243, retro_nleu_1291, retro_nleu_153, retro_nleu_157, retro_nleu_1632, retro_nleu_178 , retro_nleu_1833, retro_nleu_1903, retro_nleu_1959, retro_nleu_2145, retro_nleu_2345, retro_nleu_2381, retro_nleu_2699, retro_nleu_2965, retro_nleu_2995, retro_nleu_2996, retro_nleu_3027, retro_nleu_3028, retro_nleu_3059, retro_nleu_3111, retro_nleu_385, retro_nleu_453, retro_nleu_644, retro_nleu_805, retro_nleu_842, retro_nleu_991,
Otolemur garnettii	ENSOGAG00000004551	6 retrocopies	retro_ogar_1160, retro_ogar_1681, retro_ogar_2390, retro_ogar_2519, retro_ogar_294, retro_ogar_470,
Pteropus vampyrus	ENSPVAG00000001569	1 retrocopy	retro_pvam_17,
Rattus norvegicus	ENSRNOG00000011494	1 retrocopy	retro_rnor_259,
Sarcophilus harrisii	ENSSHAG00000013479	1 retrocopy	retro_shar_467,