RetrogeneDB ID: retro_nleu_2827

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397443.1:1132437..1133173(+)
• Located in intron of: ENSNLEG00000008588

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSNLEG00000012295
• Aliases: None
• Description: None

Sequence

>retro_nleu_2827
ATGGCGTTTCTCCGAAGCATGTGGGGCGTGCTGAGGGCCCTGGGAAGGTCTGGGCGGAGCTGTGTACCACCTGTGGAAGT
CGGCCGCACTTCCCCTTCAGTTTTATATATTTATGGAAATGGTTTTTGCCTGTCTTGGCAAGTTATCCAAAGAAACCTGT
AACTTCTTACCTTCAATTTTCTAAAGAACAACTACCCATATTTAAAGCTCAGAACCCAGATGCAAAAAATACAGAACTAA
TTAGAAGAATCACCAAGCATTGGAGGGAACTTCCCAATTCAGAGGGAAAAAATATATGAAGATGCTTATAAGGTGGACTT
GCAGGCATACAAAGAAGAGATAAGCAGAATTCAAGAACAGCTAACTCCAAGTCAGATTATGTCTTTGGAAAAAGAAATCA
TGCAGGAACATTTAAAAAGGAAAGCTTTATTAAAAAAGAGAGTTAACACTGCTTGGAAAACCAAAATGACCTCGTTCAGC
TTATAACATTTATGTAGCTGAAAGCTTCCAAGAAGCTAAGGATGGTTCACCGCAGGCAAGGCTGAAGACTGTAAACGAAA
ACTGGAAAAATCTGTTTGGTTCTCAAAAGAAAGTTTATATCCAACTTGCTAAAGATGATAAAATTCATTATTATAATGAA
ATGAAGTCTTGGGAAGAACAAATGATTGAAGTTGGATGAAAGGATCTTCTACGTCGCAAAATAAAGCAACCACCAAAAGA
TGGCACTGAGAAGTGT

Alignment

ORF - retro_nleu_2827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAFLRSMWGVLSALGRSG-AELCVGCGSRLRSPFSFVYLPRWFSSVLASCPKKPISSYLRFSKEQLPRTQ
          MAFLRSMWGVL.ALGRSG.AELC..CGSR...PFSF.YL..WF..VLAS.PKKP..SYL.FSKEQLP...
Retrocopy MAFLRSMWGVLRALGRSG<AELCTTCGSRPHFPFSFIYLWKWFLPVLASYPKKPVTSYLQFSKEQLPIFK

Parental  FHSIDTKTTELIRRIAQRWRELPDS-KKKIYQDAYKAEWQVYKEEISRFKEQLTPSQITSLEKEIMDKHL
          ....D.K.TELIRRI...WRELP.S...KIY.DAYK...Q.YKEEISR..EQLTPSQI.SLEKEIM..HL
Retrocopy AQNPDAKNTELIRRITKHWRELPNS>REKIYEDAYKVDLQAYKEEISRIQEQLTPSQIMSLEKEIMQEHL

Parental  K-KKAMTKK-KELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKENWKNLSDSEKELYIRHAKE
          K.K....KK..ELTLLGKPK.PRSAYN.YVAE.FQEAK..SPQ..LKTV.ENWKNL..S.K..YI..AK.
Retrocopy K<KESFIKK<RELTLLGKPK*PRSAYNIYVAESFQEAKDGSPQARLKTVNENWKNLFGSQKKVYIQLAKD

Parental  DETRYHNEMKCWEEQMIEVGRKDLLRRTIKQRRKYGAEEC
          D...Y.NEMK.WEEQMIEVG.KDLLRR.IKQ..K.G.E.C
Retrocopy DKIHYYNEMKSWEEQMIEVG*KDLLRRKIKQPPKDGTEKC

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_2827 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 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000535	1 retrocopy	retro_dnov_536,
Dipodomys ordii	ENSDORG00000014013	2 retrocopies	retro_dord_415, retro_dord_691,
Erinaceus europaeus	ENSEEUG00000006119	3 retrocopies	retro_eeur_103, retro_eeur_182, retro_eeur_652,
Homo sapiens	ENSG00000108064	2 retrocopies	retro_hsap_3692, retro_hsap_923,
Gorilla gorilla	ENSGGOG00000004948	2 retrocopies	retro_ggor_2496, retro_ggor_745,
Loxodonta africana	ENSLAFG00000012891	1 retrocopy	retro_lafr_1164,
Macropus eugenii	ENSMEUG00000008802	1 retrocopy	retro_meug_190,
Macaca mulatta	ENSMMUG00000019829	1 retrocopy	retro_mmul_1121,
Nomascus leucogenys	ENSNLEG00000012295	2 retrocopies	retro_nleu_2827 , retro_nleu_288,
Oryctolagus cuniculus	ENSOCUG00000014405	1 retrocopy	retro_ocun_1278,
Pongo abelii	ENSPPYG00000002430	2 retrocopies	retro_pabe_3042, retro_pabe_796,
Pan troglodytes	ENSPTRG00000002519	1 retrocopy	retro_ptro_641,
Rattus norvegicus	ENSRNOG00000000613	1 retrocopy	retro_rnor_1936,
Tursiops truncatus	ENSTTRG00000009246	1 retrocopy	retro_ttru_1763,