RetrogeneDB ID: retro_nleu_2295

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397342.1:4515141..4515847(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDCA7
• Ensembl ID: ENSNLEG00000005787
• Aliases: None
• Description: None

Sequence

>retro_nleu_2295
AGCTTCCCTGGTTTGTTCCCTGGAAGACATTCCCCGCCAGGCCCCAGCTCACAATCAAAGAGACCCCAATGTAAACATTC
CTGGGTGTTGCTTCAAGGAGACATTCTGAATGGGGAGAGCTCGGCTTCTTAGAGGTCAAGGTCAGGATCCTCGGGTCCCT
TGGCGCTCTACCTACGGAAGAGAAGGAAGAAAAGACAGAGGATAAGTACATGTTGGTGAGAAAGAGGAAGATTGTGGACG
GCTACATGAACGAAGTTGAGATGCCCAGAAATCGTCCCGCCAGATCACCCATGATCCTTCCACATATAATTCGCCCACCG
GAAGAAATTACAGAGGAAGGTTTGGAGAACATCTGCAGCAACTCTCAAGAGAAGATATATAACCGTTCGCTGGGTTCTAT
TTGCCATCAACGCCGCCAGAAAACTATTGTTACCAAAACAAACTGCAGAAACCCAGACTGCTGGGGCTTTCTAGGCCTGT
TCTGCGGCCCCGACCTTAGAAACCCTTGTGGTGAAGAGGTCAGGAATGCTCTGCTGGATGCGAACTGGCATTGCCCGCCT
TGCCGAGGACCTGCAACTGCAGTTTCCGCCTGCAGCGAGATAGACTGTGGGGAACTGGGGTCCTTGTATATTTAGCCAAA
TATAATGGCTTTGGGAATGTGCATGCTTACTTGAAAAGTCTGAAACAGGAATTTGAAATGCAAGCA

Alignment

ORF - retro_nleu_2295 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.85 %
• Parental protein coverage: 52. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SFPGSFRGRHPLPGSNSQSRRPRRR-TFPGVASRRNPERRARPLTRSRSRILGSLDALPMEEEEE--EDK
          SFPG.F.GRH..PG..SQS.RP....TF.GVASRR..E...........RILGSL.ALP.EE.EE..EDK
Retrocopy SFPGLFPGRHSPPGPSSQSKRPQCK<TFLGVASRRHSEWGELGFLEVKVRILGSLGALPTEEKEEKTEDK

Parental  YMLVRKRKTMNGYMNEDDLPRSRRSRSSMTLPHIIRPVEEISEEELENICSNSREKIYNSSLGSTCHQCR
          YMLVRKRK...GYMNE...PR.R..RS.M.LPHIIRP.EEI.EE.LENICSNS.EKIYN.SLGS.CHQ.R
Retrocopy YMLVRKRKIVDGYMNEVEMPRNRPARSPMILPHIIRPPEEITEEGLENICSNSQEKIYNRSLGSICHQRR

Parental  QKTIDTKTNCRNPDCWGVRGQFCGPCLRNRYGEEVRDALLDPNWRCPPCRG-ICNCSFCRQRDGRCATGV
          QKTI.TKTNCRNPDCWG..G.FCGP.LRN..GEEVR.ALLD.NW.CPPCRG..CNCSF..QRD....TGV
Retrocopy QKTIVTKTNCRNPDCWGFLGLFCGPDLRNPCGEEVRNALLDANWHCPPCRG<TCNCSFRLQRDRLWGTGV

Parental  LVYLAKYHGFGNVHAYLKSLKQEFEMQA
          LVYLAKY.GFGNVHAYLKSLKQEFEMQA
Retrocopy LVYLAKYNGFGNVHAYLKSLKQEFEMQA

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_2295 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007809	1 retrocopy	retro_cjac_4087,
Cavia porcellus	ENSCPOG00000011784	2 retrocopies	retro_cpor_661, retro_cpor_691,
Homo sapiens	ENSG00000144354	1 retrocopy	retro_hsap_3438,
Mus musculus	ENSMUSG00000055612	2 retrocopies	retro_mmus_1493, retro_mmus_1494,
Nomascus leucogenys	ENSNLEG00000005787	1 retrocopy	retro_nleu_2295 ,
Pan troglodytes	ENSPTRG00000012645	1 retrocopy	retro_ptro_2331,
Ictidomys tridecemlineatus	ENSSTOG00000009026	1 retrocopy	retro_itri_369,