RetrogeneDB ID: retro_nleu_921

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397276.1:36232321..36233063(+)
• Located in intron of: ENSNLEG00000006174

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPM3
• Ensembl ID: ENSNLEG00000010990
• Aliases: None
• Description: tropomyosin 3 [Source:HGNC Symbol;Acc:12012]

Sequence

>retro_nleu_921
ATGGCTGGGATCACCACCATCGAGGCAGTGAAGCACAAGATCCAGGTTCTGCTGCACCAGGCAGGTGATGCAGAGGAGCG
AGCTGAGTGCTTCCAGTGAGAAGCTGAGGGAGAAAGGCGGGCCCGGGAACAGGCTGAGGCTGAGGTGGCCTCCGTGAACG
GTAGGATCCAGCTGGTTGAAGAAGAGCTGGACTGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCA
GGAAAAGCTGCTGATGAGAGTGAGAGAGATATAAACGTTATTGAAATCTGGGTCTTAAAAGATGAAGAAGATGGAACTCC
AGGAAATCCAACTCAATGAAGCTAAGCACATTGCAGAAGAGGCAGATAGGAAGTATGAAGAGGTGGCTCATAAGTTGGTG
ATTATTGAAGGAGACATGGAATGCACAGAGGAATGAGCTGAGCTGGCAGAATCCCATTATTGAGAGATGGATGAGCAGAT
CAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCAGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATGTGAGGAAA
AGATGAAGATTCTTACTGATAATCTCAAGGAGGCAGAGACCCGTGCTGAGTTTGCTGAGAGATCGGTAGCCAAGCTGGAA
AAGACAATTGATGACTTGGAAGATAAACTGAAATGCACCAAAGAGGAACACCTCTGTACACACAGGATGCTGGACCAGAC
TCCGCTTGACCTGAATGAGATG

Alignment

ORF - retro_nleu_921 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MAGITTIEAVK.KIQVL..QA.DAEERAE..Q.E.EGERRAREQAEAEVAS.N.RIQLVEEELD.AQERL
Retrocopy MAGITTIEAVKHKIQVLLHQAGDAEERAECFQ*EAEGERRAREQAEAEVASVNGRIQLVEEELDCAQERL

Parental  ATALQKLEEAEKAADESERGMKVIE-NRALK-DEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEG
          ATALQKLEEA.KAADESER...VIE.N..LK....KMELQEIQL.EAKHIAEEADRKYEEVA.KLVIIEG
Retrocopy ATALQKLEEAGKAADESERDINVIE<NLGLK<KMKKMELQEIQLNEAKHIAEEADRKYEEVAHKLVIIEG

Parental  DLERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAER
          D.E.TEE.AELAES...EMDEQIRLMDQNLKCLSAAEEKYSQKEDK.EE..KILTD.LKEAETRAEFAER
Retrocopy DMECTEE*AELAESHY*EMDEQIRLMDQNLKCLSAAEEKYSQKEDKCEEKMKILTDNLKEAETRAEFAER

Parental  SVAKLEKTIDDLEDELYAQKLKYKAISEELDHALNDMTSI
          SVAKLEKTIDDLED.L...K.........LD....D....
Retrocopy SVAKLEKTIDDLEDKLKCTKEEHLCTHRMLDQTPLDLNEM

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_921 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 9 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Nomascus leucogenys	ENSNLEG00000005413	2 retrocopies	retro_nleu_1952, retro_nleu_469,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921 , retro_nleu_922,
Otolemur garnettii	ENSOGAG00000025133	1 retrocopy	retro_ogar_62,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318, retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,