RetrogeneDB ID: retro_nleu_2373

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397348.1:7334148..7335001(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT7
• Ensembl ID: ENSNLEG00000002489
• Aliases: None
• Description: None

Sequence

>retro_nleu_2373
ATGCCAGCAGCAACTGTACATCATAGCCAAAGAATTTGTGAAGTTTGGGCTTGCAACATGGATGAAGAGACGAAGAAAAT
TCGTCAAGTTATCCGAAAATATAATTACGTTGCTATGGACACCGAGTTTCCAGGTGTGGTTGCAAGACCCATTGGAGAAT
TCAGGAGCAATGCTGACTATCAATACCAACTATTGCAGTGTAATGTAGACTTGTTAAAGATAATTCAGCTAGGACTGACG
TTTATAAATGAGCAAGGAGAATACCCTCCAGGAACTTCAACTTGGCAGTTTAATTTTAAATTTAATTTGACAGAGGACAT
GTATGCCCAGGACTCTATAGAGCTACTAACGACATCTGGTATCCAGTTTAAAAAACATGATGAGGAAGGAATTGAGACCC
AGTATTTTGCAGAACTTCTTATGACTTCAGGAGTGGTCCTCTGTGAAGGGGTCAAATGGTTGTCATTTCATAGCAGTTAC
AACTTTGGCTATTTAATCAAAATCCTGACCAACTCTAACTTGCCTGAAGAAGAACTTGACTTCTTTGAGATCCTTCGATT
GTTTTTACCTGTCATTTATGATGTGAAGTACCTCATGAAGAGCTGCAAAAATCTCAAAGTTGGATTACAGGAGGTGGCAG
AACAGTTAGAGCTGGCATAGATAGGACCACCACATCAGGCAGGATCTAATTCATTGCTCACAGGAATGGCCTTTTTCAAA
ATGAGAGGAATGTTCTTTGAAGATCATACTGACGATGCCAAATATTGTGTCATTTGTATGGCTTTGGTTCTGGTTCATCC
TATGTACAGAATGGCACAGGGAATCATATGAAGAAGAAGCCAACAAGCAGTCA

Alignment

ORF - retro_nleu_2373 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.68 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD
          MPAATV.HSQRICEVWACN.DEE.KKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLL.CNVD
Retrocopy MPAATVHHSQRICEVWACNMDEETKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLQCNVD

Parental  LLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELL
          LLKIIQLGLTF.NEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKH.EEGIETQYFAELL
Retrocopy LLKIIQLGLTFINEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHDEEGIETQYFAELL

Parental  MTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGLQ
          MTSGVVLCEGVKWLSFHS.Y.FGYLIKILTNSNLPEEELDFFEILRLF.PVIYDVKYLMKSCKNLK.GLQ
Retrocopy MTSGVVLCEGVKWLSFHSSYNFGYLIKILTNSNLPEEELDFFEILRLFLPVIYDVKYLMKSCKNLKVGLQ

Parental  EVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYC-GHLYGLGSGSSYVQNGTGN-AYE
          EVAEQLEL..IGP.HQAGS.SLLTGMAFFKMR.MFFEDH.DDAKYC..HLYG.GSGSSYVQNGTGN..YE
Retrocopy EVAEQLELA*IGPPHQAGSNSLLTGMAFFKMRGMFFEDHTDDAKYC<CHLYGFGSGSSYVQNGTGN<SYE

Parental  EEANKQS
          EEANKQS
Retrocopy EEANKQS

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_2373 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373 ,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730,