RetrogeneDB ID: retro_nleu_2954

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397514.1:1012600..1013312(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD2
• Ensembl ID: ENSNLEG00000004516
• Aliases: None
• Description: None

Sequence

>retro_nleu_2954
CTCATGAAAGACCAGCATTTATGAGATTCCTTCTCAGACTCCACATCATTCAATATTTTGATGGATATGTTATTTATCAA
AGGCAAATATAAAAGTGCTTTGGAAGTATTGATAGAGATGAAAAATCAAGGTGTGAAATTCACTAAAGATCCTATATTCT
TACTTTTGCAGTTTGCAACAAACTGAATAGCTCTGAGTCTTTCAAAATCTGTTCTACGTTAAGAGAAGAAGCCCTACTCA
AAGGAGAGGTTCTCTCCAGGAGAGCATCCTGTTTCTTTGTGGCATTAGCTCTGAATCAGAACCAAGTGGCAAAAGCTATG
TCCATTTTTTTCTCAAACCATGAATCCAGAAAGCATAGCCTGCACTAGTTTAACTATTATAATCCATATCCAGTCAAATA
TGTTGGAAACCCTGATAGAGATACTAAAAAAAATGCTGCAGAAGGAAATTTATTAAAATTTGTGAAAAGACATGCATTCT
CAGAGGAAGTTCTGGCAAAGGTGAAGGAAAAGTGAAGGATATGCCTGCCCTTGTGACCAGATTTAATGAGCTCTACGGAA
AACTGCACATCAGTGGCCAGGTCATCACTTGTACTTTGGGTAGTCTGCTCTGCCACACCCCCAGGGACAGGAAATCCCAT
ATGTTGCTATTAAACAAAAGGATGATGAGCCGTTAGACCTTCCAGCCACTCAACCAGTCCTTTTTGGCTGAG

Alignment

ORF - retro_nleu_2954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.83 %
• Parental protein coverage: 61.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LMKDQHLRGFFSDSTSFNILMDMLFIKGKYKSALEVLIEMKNQDVRFTKD-TYVLAFAICYKLNSPESFK
          LMKDQHL...FSDSTSFNILMDMLFIKGKYKSALEVLIEMKNQ.V.FTKD..Y.L.FA.C.KLNS.ESFK
Retrocopy LMKDQHL*DSFSDSTSFNILMDMLFIKGKYKSALEVLIEMKNQGVKFTKD<SYILTFAVCNKLNSSESFK

Parental  ICTTLREEALLKGEILSRRASCFAVALALNQNEVAKAMSI-FSQIMNPESIACTNLNIIIHIQSNMLENL
          IC.TLREEALLKGE.LSRRASCF.VALALNQN.VAKAMSI.FSQ.MNPESIACT.L.IIIHIQSNMLE.L
Retrocopy ICSTLREEALLKGEVLSRRASCFFVALALNQNQVAKAMSI>FSQTMNPESIACTSLTIIIHIQSNMLETL

Parental  IETLKNAAEENL-SKFVKRRAFSEEVLAKVREKVKDVPALVAKFDEIYGTLHITGQITTDSLDAVLCYTP
          IE............K.............K...KVKD.PALV..F.E.YG.LHI.GQ..T..L...LC.TP
Retrocopy IEIXXXXLQKEI>IKICEKTCILRGSSGKGEGKVKDMPALVTRFNELYGKLHISGQVITCTLGSLLCHTP

Parental  RDRKSHTLLLNKKMVSRRTFQPLSQSLLAE
          RDRKSH.LLLNK.M.SR.TFQPL.QS.LAE
Retrocopy RDRKSHMLLLNKRMMSR*TFQPLNQSFLAE

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_2954 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016364	1 retrocopy	retro_cjac_1598,
Homo sapiens	ENSG00000049883	2 retrocopies	retro_hsap_1388, retro_hsap_607,
Gorilla gorilla	ENSGGOG00000010695	2 retrocopies	retro_ggor_1077, retro_ggor_534,
Macaca mulatta	ENSMMUG00000017908	1 retrocopy	retro_mmul_2240,
Nomascus leucogenys	ENSNLEG00000004516	2 retrocopies	retro_nleu_2954 , retro_nleu_436,
Otolemur garnettii	ENSOGAG00000008390	1 retrocopy	retro_ogar_3169,
Pan troglodytes	ENSPTRG00000016968	2 retrocopies	retro_ptro_447, retro_ptro_952,
Ictidomys tridecemlineatus	ENSSTOG00000006596	1 retrocopy	retro_itri_1469,