RetrogeneDB ID: retro_nleu_1980

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397320.1:12669520..12670161(-)
• Located in intron of: ENSNLEG00000004522

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL10A
• Ensembl ID: ENSNLEG00000008650
• Aliases: None
• Description: Ribosomal protein [Source:UniProtKB/TrEMBL;Acc:G1RBG6]

Sequence

>retro_nleu_1980
ATGAGCATCAAAGTCTCTCGCGACACCCTGTACAAGGCAGTGTGGGAAGTCCTGCAGGGGAACCAGCGCAAGTGCCGCAA
GTTCCTGGAGATGGTGGAGTTGCAGATCAGCTTGACCCCCAGAAGGACAAGCGCTTCTCGGGCACCATCAGGCTTAAGTC
CACTCCCCACCCCAAGTTCTCTATGTGTGTCCTGGGGGACCAGCAGCACTGTGACGAGGCTAAGGCCGTGGATATCCCCC
ACATGGACATCGAGGCGCTGAAAAAACTCAACAAGAATAAAAAACTGGTCAAGAAGCTGGCCAAGAAGTATGATGCGTTT
TTGGCCTCAGAGTCTCTGATCAAGCAGATTCCACAAATCCTCGGCCCAGGTCTAAATAAGGCAGGAAAGTTCCCTTCCCT
GCTCACACACAGCAAAAACATGGGGGCCAAAGTGGATGAGGCGAAGTCCACAATCAAGTTCCAAATGAAGAAGGTGTTAT
GTCTGGCTGTAGCTGTTGGTCACGTGAAGATGACAGACGATGAGCTTGTGTATAACATTCACCTGGCTGTCAACTTCTTG
GTGTCATTGCTCAAGAAAAACTGGCAGAATGTCTGGGCCTTATATATCAAGAGCACCATGGGCAAGCCCCAGCACCTATA
T

Alignment

ORF - retro_nleu_1980 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.4 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSKVSRDTLYEAVREVLHGNQRKRRKFLETVELQISLKNYDPQKDKRFSGTVRLKSTPRP-KFSVCVLG
          MS.KVSRDTLY.AV.EVL.GNQRK.RKFLE.VELQISL....P...........L...P.P.KFS.CVLG
Retrocopy MSIKVSRDTLYKAVWEVLQGNQRKCRKFLEMVELQISL---TPRRTSASRAPSGLSPLPTP<KFSMCVLG

Parental  DQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPRILGPGLNKAGKFPSLLT
          DQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIP.ILGPGLNKAGKFPSLLT
Retrocopy DQQHCDEAKAVDIPHMDIEALKKLNKNKKLVKKLAKKYDAFLASESLIKQIPQILGPGLNKAGKFPSLLT

Parental  HNENMVAKVDEVKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVRALYIKST
          H..NM.AKVDE.KSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNV.ALYIKST
Retrocopy HSKNMGAKVDEAKSTIKFQMKKVLCLAVAVGHVKMTDDELVYNIHLAVNFLVSLLKKNWQNVWALYIKST

Parental  MGKPQRLY
          MGKPQ.LY
Retrocopy MGKPQHLY

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_1980 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 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000670	13 retrocopies	retro_amel_1144, retro_amel_1223, retro_amel_1262, retro_amel_1591, retro_amel_1813, retro_amel_198, retro_amel_318, retro_amel_320, retro_amel_417, retro_amel_520, retro_amel_609, retro_amel_710, retro_amel_970,
Echinops telfairi	ENSETEG00000013325	2 retrocopies	retro_etel_1974, retro_etel_326,
Felis catus	ENSFCAG00000012904	7 retrocopies	retro_fcat_1144, retro_fcat_1488, retro_fcat_1561, retro_fcat_1971, retro_fcat_210, retro_fcat_262, retro_fcat_560,
Homo sapiens	ENSG00000198755	13 retrocopies	retro_hsap_142, retro_hsap_1462, retro_hsap_1710, retro_hsap_177, retro_hsap_1935, retro_hsap_2795, retro_hsap_3025, retro_hsap_3245, retro_hsap_3353, retro_hsap_337, retro_hsap_3949, retro_hsap_4025, retro_hsap_4040,
Gorilla gorilla	ENSGGOG00000028140	10 retrocopies	retro_ggor_1, retro_ggor_1124, retro_ggor_1282, retro_ggor_1407, retro_ggor_2088, retro_ggor_2273, retro_ggor_234, retro_ggor_2702, retro_ggor_358, retro_ggor_57,
Macropus eugenii	ENSMEUG00000005760	6 retrocopies	retro_meug_1337, retro_meug_1578, retro_meug_2066, retro_meug_407, retro_meug_541, retro_meug_705,
Macaca mulatta	ENSMMUG00000015907	6 retrocopies	retro_mmul_1931, retro_mmul_2041, retro_mmul_2321, retro_mmul_2330, retro_mmul_306, retro_mmul_583,
Monodelphis domestica	ENSMODG00000013766	2 retrocopies	retro_mdom_276, retro_mdom_499,
Nomascus leucogenys	ENSNLEG00000008650	13 retrocopies	retro_nleu_1174, retro_nleu_1210, retro_nleu_1697, retro_nleu_1778, retro_nleu_1980 , retro_nleu_2055, retro_nleu_2342, retro_nleu_2436, retro_nleu_2879, retro_nleu_662, retro_nleu_838, retro_nleu_986, retro_nleu_989,
Ornithorhynchus anatinus	ENSOANG00000014574	1 retrocopy	retro_oana_86,
Oryctolagus cuniculus	ENSOCUG00000004065	2 retrocopies	retro_ocun_130, retro_ocun_4,
Rattus norvegicus	ENSRNOG00000000505	4 retrocopies	retro_rnor_2302, retro_rnor_37, retro_rnor_400, retro_rnor_43,
Sarcophilus harrisii	ENSSHAG00000002047	1 retrocopy	retro_shar_438,
Tursiops truncatus	ENSTTRG00000009431	6 retrocopies	retro_ttru_100, retro_ttru_1137, retro_ttru_1325, retro_ttru_1477, retro_ttru_205, retro_ttru_494,