RetrogeneDB ID: retro_nleu_1479

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397295.1:7190325..7190564(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM6
• Ensembl ID: ENSNLEG00000005584
• Aliases: None
• Description: None

Sequence

>retro_nleu_1479
ATGAGTCTTCAGAAGCAAACCTCTGGTGACTCTTAAAGCAAATCATGGGTCAGCCAACTGTTGGTAAAATTAAATTCTGC
AGTGGATTATTGAGGCGTCCTGGCTTGCCTGGATGGCTACATGAATATAGCCCTGAAGCAGGCGGAAGAATATGTAATGG
ACAACTGAAGAATAAGCATGGGGTTGCATTTAGCCACAGAAACCATGTGTTCTACATCAGTGCACAGAAGAAAAGGATG

Alignment

ORF - retro_nleu_1479 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSLRKQTPSD-FLKQIIGRPVV-VKLNSGVDYRGVLACLDGYMNIALEQTEEYV-NGQLKNKYGDAFIRG
          MSL.KQT..D..LKQI.G.P.V.VKLNS.VDY.GVLACLDGYMNIAL.Q.EEYV.NGQLKNK.G.AF...
Retrocopy MSLQKQTSGD<LLKQIMGQPTV>VKLNSAVDY*GVLACLDGYMNIALKQAEEYV<NGQLKNKHGVAFSHR

Parental  NNVLYISTQKRRM
          N.V.YIS.QK.RM
Retrocopy NHVFYISAQKKRM

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_1479 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014060	1 retrocopy	retro_btau_861,
Cavia porcellus	ENSCPOG00000015389	1 retrocopy	retro_cpor_368,
Dasypus novemcinctus	ENSDNOG00000009322	5 retrocopies	retro_dnov_1118, retro_dnov_176, retro_dnov_2092, retro_dnov_301, retro_dnov_664,
Homo sapiens	ENSG00000164167	2 retrocopies	retro_hsap_1948, retro_hsap_2107,
Gorilla gorilla	ENSGGOG00000001310	2 retrocopies	retro_ggor_1417, retro_ggor_1638,
Myotis lucifugus	ENSMLUG00000026355	1 retrocopy	retro_mluc_1859,
Monodelphis domestica	ENSMODG00000000526	4 retrocopies	retro_mdom_1027, retro_mdom_1383, retro_mdom_1983, retro_mdom_621,
Nomascus leucogenys	ENSNLEG00000005584	2 retrocopies	retro_nleu_1275, retro_nleu_1479 ,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Otolemur garnettii	ENSOGAG00000026665	1 retrocopy	retro_ogar_233,
Sus scrofa	ENSSSCG00000009036	2 retrocopies	retro_sscr_474, retro_sscr_475,
Tarsius syrichta	ENSTSYG00000012759	4 retrocopies	retro_tsyr_1332, retro_tsyr_1727, retro_tsyr_340, retro_tsyr_653,