RetrogeneDB ID: retro_nleu_640

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397269.1:21119976..21120548(+)
• Located in intron of: ENSNLEG00000004347

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUGT1
• Ensembl ID: ENSNLEG00000015700
• Aliases: None
• Description: None

Sequence

>retro_nleu_640
AGTGCAGATGCTAATTTCAGTGTCTGGATTAAAAGGTGTTAAGAAGCTCAGAATGGCCCAGAATCTGAGGTGTGGACTCA
TCAGTCAAAAATCAAGTATGACTGGTATCAAACAGAATCTCAAGTAGTCATTACACTTATGATCAAGAATGTTCAAAGAA
TGATGTAAATGTGGAATTTTCAGAAAAAGAATTGTCTGCTTTGGTTAAACTTCCTTCTGGAGAGGATTACAATTTTAAAC
TGGAACTTCATCCTATAATACCAGAACAGAGCATATTTAAAGTAGTTTCAACAAAGATTGAAATCAAACTGAAAAAGCCA
GAGGCTGTGAGATGGGAAAAGCTAGAGGGGCAAGGAGATGTGCCTACACCAAAACAATTCATAGCAGGTGTAAAGAACCT
ACATCCATCATCATCTCCTTATACAAGAAATTGGGATAAATTAGTGGGTAAAATCAAAGAAGAAGAAAATAATGAAAAGT
TGGAGGGAGATGCAGCTTTAAACAGATGATTTCAGCAGATCTCTTCAGATGGTTCTGATGAAGTGAAATGTGCCATGAAC
CAATCCTTTGTG

Alignment

ORF - retro_nleu_640 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.19 %
• Parental protein coverage: 63.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SADANFSIWIKRCQEAQNGSESEVWTHQSKIKYDWYQTESQVVITLMIKNVQ-KNDVNVEFSEKELSALV
          SADANFS.WIKRC.EAQNG.ESEVWTHQSKIKYDWYQTESQVVITLMIKNVQ.KNDVNVEFSEKELSALV
Retrocopy SADANFSVWIKRC*EAQNGPESEVWTHQSKIKYDWYQTESQVVITLMIKNVQ<KNDVNVEFSEKELSALV

Parental  KLPSGEDYNLKLELLHPIIPEQSTFKVLSTKIEIKLKKPEAVRWEKLEGQGDVPTPKQFVADVKNLYPSS
          KLPSGEDYN.KLEL.HPIIPEQS.FKV.STKIEIKLKKPEAVRWEKLEGQGDVPTPKQF.A.VKNL.PSS
Retrocopy KLPSGEDYNFKLEL-HPIIPEQSIFKVVSTKIEIKLKKPEAVRWEKLEGQGDVPTPKQFIAGVKNLHPSS

Parental  SPYTRNWDKLVGEIKEEEKNEKLEGDAALNRLFQQIYSDGSDEVKRAMNKSFV
          SPYTRNWDKLVG.IKEEE.NEKLEGDAALNR.FQQI.SDGSDEVK.AMN.SFV
Retrocopy SPYTRNWDKLVGKIKEEENNEKLEGDAALNR*FQQISSDGSDEVKCAMNQSFV

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_640 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 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008606	2 retrocopies	retro_amel_353, retro_amel_896,
Canis familiaris	ENSCAFG00000004823	1 retrocopy	retro_cfam_136,
Callithrix jacchus	ENSCJAG00000003604	1 retrocopy	retro_cjac_310,
Cavia porcellus	ENSCPOG00000003374	1 retrocopy	retro_cpor_110,
Dasypus novemcinctus	ENSDNOG00000002991	1 retrocopy	retro_dnov_2621,
Homo sapiens	ENSG00000165416	1 retrocopy	retro_hsap_2628,
Gorilla gorilla	ENSGGOG00000006797	1 retrocopy	retro_ggor_1840,
Nomascus leucogenys	ENSNLEG00000015700	1 retrocopy	retro_nleu_640 ,
Otolemur garnettii	ENSOGAG00000008220	1 retrocopy	retro_ogar_41,
Pan troglodytes	ENSPTRG00000005906	1 retrocopy	retro_ptro_1773,