RetrogeneDB ID: retro_nleu_586

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397267.1:43030155..43031012(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC137
• Ensembl ID: ENSNLEG00000013830
• Aliases: None
• Description: None

Sequence

>retro_nleu_586
GTGGCCCGGGCTTCGCAGGTGACAGCGCTGCCCCGCGAGGCCGCCACACTTCCCCAGAGAAGGGGACACCTTGAAGGCTC
CGCCCGGGACCCCCTAGGGAGCGTTCACTGGGACCCCTTCCCCAGCAAAGAGAAGAAGAAAGTGAACTGCAAGCCCAAGA
ACTAGGACGAACAAGAGATCCCTTTCCAGCTCCGGGAGATTATGAGGAGCCGCCAGGAGATGAAACACCCGATCAGTAAC
AAGAAAAGGAAGAAAGCAGCCCAGGTGACCTTCAGAAAGACATCGGAGAAGGAAGCAAAGGGAGTGGAGCCTGACATCGC
CGTCCCCAAGTTCAAACAGAGGAAGAGGGAGTCTGACGGGGCCTATATCCAGCGCATGCAGCAAGAGGCCCAGCACGTGC
TATTCTTCAGCAAGAACAAGGCCATCCTGCAGCCAGAGGTGCAGGCAGCTCCCAAGGAGAAGTCTGAGTAGAAAAAAGCA
AAAAAAGCATTCCAGAAGCGGCGACTAGATAAAGTCCGACGGAAAAAGGAGGAAAAGGCGGGAGACAGGCTGGAGCAGAG
CTGCTTCGAGACACGGTGAAGTTTGGTGAGGTTGTCCTGCAGCCCCCAGAGCTGACTGCCAGGCCCCGGAGGAGTGTAAG
CAAGGACCAGCCTGGCAGGAGATCGCAGATGCTGAGGATGCTTCTGAGCCCAGGCGGTGTGTCCCAGCCTCTGACCGCCT
CCCTGGCCTGCCAGCGGATTGTGGGGGAGGAGAGAGAGCAGGCGGTGCAGGCCTACAGAGTGTTGAAGCGGCGGCGGCGG
CGGCTGCATGGGGAGCAACCCCACCTCACTTCCTGGAAGAAGCCAGAGCCGCAGCTG

Alignment

ORF - retro_nleu_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.66 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MARAGQGAAVPRVQAGPGSPRRARRRQQVQPLGKQRPAPWPGLRSKEKKKVNCKPKNQDEQEIPFRLREI
          .ARA.Q..A.PR..A.....R.........PLG.....P.P...SKEKKKVNCKPKN.DEQEIPF.LREI
Retrocopy VARASQVTALPREAATLPQRRGHLEGSARDPLGSVHWDPFP---SKEKKKVNCKPKN*DEQEIPFQLREI

Parental  MRSRQEMKNPISNKKRKKAAQVTFRKTLEKEAKGAEPDIAIPKFKQRKGESDGAYIQRMQQEAQHVLFLS
          MRSRQEMK.PISNKKRKKAAQVTFRKT.EKEAKG.EPDIA.PKFKQRK.ESDGAYIQRMQQEAQHVLF.S
Retrocopy MRSRQEMKHPISNKKRKKAAQVTFRKTSEKEAKGVEPDIAVPKFKQRKRESDGAYIQRMQQEAQHVLFFS

Parental  KNQAIRQPEMQAAPKEKSEQKKAKKAFQKRRLDKVRRKKEEKAADRLEQ-ELLQDMVKFGEVVLQPPELT
          KN.AI.QPE.QAAPKEKSE......AFQKRRLDKVRRKKEEKA.DRLEQ.ELL.D.VKFGEVVLQPPELT
Retrocopy KNKAILQPEVQAAPKEKSE*XXXXXAFQKRRLDKVRRKKEEKAGDRLEQ<ELLRDTVKFGEVVLQPPELT

Parental  ARPRRSVSKDQPGRRSQMPRMLLNPGCVSQPLTASLARQRIVGEERERAVQAYRVLKQRRRRLHGEQPHL
          ARPRRSVSKDQPGRRSQM.RMLL.PG.VSQPLTASLA.QRIVGEERE.AVQAYRVLK.RRRRLHGEQPHL
Retrocopy ARPRRSVSKDQPGRRSQMLRMLLSPGGVSQPLTASLACQRIVGEEREQAVQAYRVLKRRRRRLHGEQPHL

Parental  TSRKKAEPQL
          TS.KK.EPQL
Retrocopy TSWKKPEPQL

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_586 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014878	1 retrocopy	retro_eeur_523,
Homo sapiens	ENSG00000185298	1 retrocopy	retro_hsap_2661,
Gorilla gorilla	ENSGGOG00000009333	1 retrocopy	retro_ggor_1857,
Macaca mulatta	ENSMMUG00000008831	1 retrocopy	retro_mmul_1511,
Monodelphis domestica	ENSMODG00000002713	1 retrocopy	retro_mdom_1355,
Mus musculus	ENSMUSG00000049957	1 retrocopy	retro_mmus_641,
Nomascus leucogenys	ENSNLEG00000013830	3 retrocopies	retro_nleu_1264, retro_nleu_1530, retro_nleu_586 ,
Pongo abelii	ENSPPYG00000008741	1 retrocopy	retro_pabe_2312,
Pan troglodytes	ENSPTRG00000009767	1 retrocopy	retro_ptro_1793,
Rattus norvegicus	ENSRNOG00000048712	1 retrocopy	retro_rnor_472,