RetrogeneDB ID: retro_nleu_2008

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397322.1:14073218..14073595(+)
• Located in intron of: ENSNLEG00000010224

Retrocopy information

• Ensembl ID: ENSNLEG00000010239
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FAM18B1
• Ensembl ID: ENSNLEG00000014658
• Aliases: None
• Description: None

Sequence

>retro_nleu_2008
AAGAATGTCACAGGTAGACTGATGGTTGGCCTACGTTGGTGGAATCACACTGTGAAGATGGAAAGAGCCATTGGGTGTTT
GAATCTAGAAAGGAGTCCTCTGAAGAGAATAAAACTGTGTCAGAGGCTGAATCAGGAATCTTTTGGTTGGGACTTACTGC
CTGTCCAGTGCTGTGGGTGATATTTGCCTTTAGTGCACTCTTCTCCTTCAGAGTAAAGTGGTTGCCAGTGGTTATCATGG
GTGTGGTGCTACAAGGTGCCAACCTCTATGGTTACATCAGGTGTAAGGTGGGCAGCAGAAAGAATTTAACCAGCATGGCT
ACTTTATATTTTGGAAAGCAATTTTTAAGACAAAACACTGGAGATGATCAGACTTCC

Alignment

ORF - retro_nleu_2008 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QNVTGRLMVGLRWWNHID-EDGKSHWVFESRKESSQENKTVSEAESRIFWLGLIACPVLWVIFAFSALFS
          .NVTGRLMVGLRWWNH...EDGKSHWVFESRKESS.ENKTVSEAES.IFWLGL.ACPVLWVIFAFSALFS
Retrocopy KNVTGRLMVGLRWWNHTV<EDGKSHWVFESRKESSEENKTVSEAESGIFWLGLTACPVLWVIFAFSALFS

Parental  FRVKWLAVVIMGVVLQGANLYGYIRCKVGSRKNLTSMATSYFGKQFLRQNTGDDQSS
          FRVKWL.VVIMGVVLQGANLYGYIRCKVGSRKNLTSMAT.YFGKQFLRQNTGDDQ.S
Retrocopy FRVKWLPVVIMGVVLQGANLYGYIRCKVGSRKNLTSMATLYFGKQFLRQNTGDDQTS

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_2008 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 13 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Microcebus murinus	ENSMICG00000015098	4 retrocopies	retro_mmur_1331, retro_mmur_151, retro_mmur_161, retro_mmur_683,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Macaca mulatta	ENSMMUG00000019203	5 retrocopies	retro_mmul_1032, retro_mmul_2125, retro_mmul_278, retro_mmul_600, retro_mmul_748,
Nomascus leucogenys	ENSNLEG00000010137	1 retrocopy	retro_nleu_2447,
Nomascus leucogenys	ENSNLEG00000014658	2 retrocopies	retro_nleu_1961, retro_nleu_2008 ,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000, retro_tsyr_530,