RetrogeneDB ID: retro_nleu_2248

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397338.1:2965473..2966149(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNH
• Ensembl ID: ENSNLEG00000013604
• Aliases: None
• Description: None

Sequence

>retro_nleu_2248
TATCACTCCTGGATAATAATGCTCACATGTGTATTTTTGGCCTACAAAGTAGATAAACTGAATGTATCTAGTCCCCACTT
TGTTGGAAACCTTCGGGAGAGTTCTCTTGTACAGGAGGAGACACTTGAACAGAGTTTGGAATATGAACTACATTTTACAC
AGCAACTTCAATTTCCATCTGACTGTCCACAACCCCTATAGACCACTGGAGTGCTTCCTCACTGATTTAAAGACTTACTG
TGCAATGCTGGAGAATCCAGACATTTTGAGGAAAACAGATGATGAAGTTCTTAATAGAATCACATTGGTGGCTGCTTACC
ATTTATACACACCTTCCCAAATTGCCCTGCCTGCCATTTTATCTAGTGCCTTCAGGGCTGGAATTACTATGGAAAGTTAT
TTATTGGACAGTCTGATGTTGAGAGAGAACAGAACTTGCTTGTCACAGTTACTAGATATAATGAAAAGCATGAGAAATTG
AGTAAAAAAGTATGTACCACCCAGATCTGAAGAAGCTGCTGTTCTGAAACCGAAGTTGGAGCAATGTCATTCGGCTGAGC
TCGCACTTAATGTAATTATGACGAAGAGGAAAGGCTGTGAAGATAATGATGATGTCTCAAAGAAATCCAGACATGAGGAG
GAAGAATAGACTGATGATGACCTGGTAGACTCTCTC

Alignment

ORF - retro_nleu_2248 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.32 %
• Parental protein coverage: 69.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YHPRIIMLTCAFLACKVDEFNVSSPQFVGNLRESPLGQEKALEQILEYELLLIQQL-NFHLIVHNPYRPF
          YH..IIMLTC.FLA.KVD..NVSSP.FVGNLRES.L.QE..LEQ.LEYEL...QQL.NFHL.VHNPYRP.
Retrocopy YHSWIIMLTCVFLAYKVDKLNVSSPHFVGNLRESSLVQEETLEQSLEYELHFTQQL>NFHLTVHNPYRPL

Parental  EGFLIDLKTRYPILENPEILRKTADDFLNRIALTDAYLLYTPSQIALTAILSSASRAGITMESYLSESLM
          E.FL.DLKT....LENP.ILRKT.D..LNRI.L..AY.LYTPSQIAL.AILSSA.RAGITMESYL..SLM
Retrocopy ECFLTDLKTYCAMLENPDILRKTDDEVLNRITLVAAYHLYTPSQIALPAILSSAFRAGITMESYLLDSLM

Parental  LRENRTCLSQLLDIMKSMRNLVKKYEPPRSEEVAVLKQKLERCHSAELALNVITKKRKGYEDDDYVSKKS
          LRENRTCLSQLLDIMKSMRN.VKKY.PPRSEE.AVLK.KLE.CHSAELALNVI..KRKG.ED.D.VSKKS
Retrocopy LRENRTCLSQLLDIMKSMRN*VKKYVPPRSEEAAVLKPKLEQCHSAELALNVIMTKRKGCEDNDDVSKKS

Parental  KHEEEEWTDDDLVESL
          .HEEEE.TDDDLV.SL
Retrocopy RHEEEE*TDDDLVDSL

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_2248 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007765	1 retrocopy	retro_dnov_1618,
Homo sapiens	ENSG00000134480	1 retrocopy	retro_hsap_3128,
Gorilla gorilla	ENSGGOG00000005172	1 retrocopy	retro_ggor_2143,
Macaca mulatta	ENSMMUG00000003248	1 retrocopy	retro_mmul_1991,
Mus musculus	ENSMUSG00000021548	1 retrocopy	retro_mmus_2510,
Nomascus leucogenys	ENSNLEG00000013604	1 retrocopy	retro_nleu_2248 ,
Oryctolagus cuniculus	ENSOCUG00000004659	1 retrocopy	retro_ocun_588,
Pongo abelii	ENSPPYG00000015619	2 retrocopies	retro_pabe_2584, retro_pabe_2590,
Pan troglodytes	ENSPTRG00000017063	1 retrocopy	retro_ptro_2116,
Ictidomys tridecemlineatus	ENSSTOG00000000659	1 retrocopy	retro_itri_856,