RetrogeneDB ID: retro_nleu_2940

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397498.1:11195..11712(+)
• Located in intron of: ENSNLEG00000012464

Retrocopy information

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

Parental gene information

• Parental gene symbol: BRCC3
• Ensembl ID: ENSNLEG00000014460
• Aliases: None
• Description: None

Sequence

>retro_nleu_2940
GTTCATCTCGAGTCTGACGCTTTCCTCATTTGTCTCAACCATGCTCTGAGCACAGAGAAGGAGGAAGTGATGGGGCTATG
CATAGGGGAGTTGAACGATGATACAAGGAGTGACTCCAAATTTGCATATACTGGAACTGAAATGCCCACAGTTGCTGAAA
AGGTTGATGCCTTCAGAATTGTTCGCATTCATTCTGTCATCATCTTACGACGTTCTGATAAGTGGAAGGACTGAGTAGAA
ATTTCTCCAGGGCAGCTGTCTGCAGCTTCAACAGAGGCAGAGAGGTTGGCTGAACTGACAGGCCACCCCATGAGAGTTGT
GGGCTGGTATCATTCCCACCCTCATGTAACTGTTTGGCCTTCACATGTTGATGTTCGCACACGAGCCACGTACCAGATGA
TGGATCAAGGCTTTGTAGGACTTATTTTTTTCCTGTTTCATAGAAGATAAGAAAACAAGGACTGGCCGGGTACTCTACAC
TTGCTTCCAATCCATACAGGCCCAAAAGAGTTCAGAG

Alignment

ORF - retro_nleu_2940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.91 %
• Parental protein coverage: 59.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VHLESDAFLVCLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMRTVAEKVDAVRIVHIHSVIILR
          VHLESDAFL.CLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEM.TVAEKVDA.RIV.IHSVIILR
Retrocopy VHLESDAFLICLNHALSTEKEEVMGLCIGELNDDTRSDSKFAYTGTEMPTVAEKVDAFRIVRIHSVIILR

Parental  RSDKRKDRVEISPEQLSAASTEAERLAELTGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDQGFVG
          RSDK.KD.VEISP.QLSAASTEAERLAELTG.PMRVVGWYHSHPH.TVWPSHVDVRT.A.YQMMDQGFVG
Retrocopy RSDKWKD*VEISPGQLSAASTEAERLAELTGHPMRVVGWYHSHPHVTVWPSHVDVRTRATYQMMDQGFVG

Parental  LI-FSCFIEDKNTKTGRVLYTCFQSIQAQKSSE
          LI.FSCFIEDK.T.TGRVLYTCFQSIQAQKSSE
Retrocopy LI>FSCFIEDKKTRTGRVLYTCFQSIQAQKSSE

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_2940 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327, retro_btau_1646,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388, retro_cpor_627,
Homo sapiens	ENSG00000185515	1 retrocopy	retro_hsap_3271,
Gorilla gorilla	ENSGGOG00000027248	1 retrocopy	retro_ggor_2226,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672,
Nomascus leucogenys	ENSNLEG00000014460	1 retrocopy	retro_nleu_2940 ,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51,