RetrogeneDB ID: retro_nleu_2556

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397371.1:2608502..2609162(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1IP1
• Ensembl ID: ENSNLEG00000010636
• Aliases: None
• Description: None

Sequence

>retro_nleu_2556
CTAGATACTGTCCTCACAGAACTTAGTCCATCAGAGGAATATAAAGCTATGGTATTGGCAGGAGTGCAACCAGAGATGAT
GTTGAACATTAGCTCCTGAGCACTATACTTCTGGACATATTAGGTATATCAGGAGTCTCTCTATAAGAATACAATTTCAG
CAAAGCTGAGGGCCATCCAAAACACATGGAGAAGATATATACTCAGCAAACACAGAGCAAAGACGTAGAATTGACATCTA
TAAAAGGAGAGATCACCTCCATGAAGTAAGTGCTAAAAGAACACAATAAAAATGTTCACTGGTATCTTTAAAAACTGTAT
GGAGTGCAATCAAAAGTATCAAAAAGCTCCAAAGCCTCTGTGATAGTCTGAGGCTATGAAACATTACTGTTGCTAACCAA
GAACATACCTTTGAACCATCCATAATTGCACGGTCTGGTGTTTTTTGCTTTTCATTAGGGAACAACGCCAAGTGTTTTTT
GGACAGTGTACCAGTTTAAAATCTGGGTGATGGAGATGGAGATTTTCAGTTCAGACCTTTTTTTTCTGGATTCTCACAAA
ACACCTGAAGCAAGCAATAGCTTTTTTCAGTTTTGCCGCTCCAAGTCATGAATTAGAGCAGCAGCAAGTTTCCAGCAGGG
TCGTGAAAGTGAAAACAATT

Alignment

ORF - retro_nleu_2556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.2 %
• Parental protein coverage: 79.06 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LDIVRTELSPSEEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQ-EYNFSKAEGHLKQMEKIYTQ
          LD.V.TELSPSEEYKAMVLAG..PE..L.ISS.AL.FWTY.V.QE.LY..EYNFSKAEGH.K.MEKIYTQ
Retrocopy LDTVLTELSPSEEYKAMVLAGVQPEMMLNISS*ALYFWTY*VYQESLYK<EYNFSKAEGHPKHMEKIYTQ

Parental  QIQSKDVELTSMKGEITSMKKVLEEYKKK-FSDISEKLMERNRQYQK-LQGLYDSLRLRNITIANHEGTL
          Q.QSKDVELTS.KGEITSMK.VL.E..K..F..I....ME.N..YQK.LQ.L.DSLRL.NIT.AN.E.T.
Retrocopy QTQSKDVELTSIKGEITSMK*VLKEHNKN>FTGIFKNCMECNQKYQK>LQSLCDSLRL*NITVANQEHTF

Parental  EPSMIAQSGVLGFPLGNNSKFPLDNTPVRNRGDGDGDFQFRPFFAG-SPTAPEPSNS-FFSFVSPSGELE
          EPS.IA.SGV..F.LGNN.K..LD..PV.N.GDGDGDFQFR....G.S...PE.SNS.FFSF..PS.ELE
Retrocopy EPSIIARSGVFCFSLGNNAKCFLDSVPV*NLGDGDGDFQFRXXXXG>SHKTPEASNS>FFSFAAPSHELE

Parental  QQQVSSRAFKVKRI
          QQQVSSR..KVK.I
Retrocopy QQQVSSRVVKVKTI

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_2556 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009967	2 retrocopies	retro_cjac_3244, retro_cjac_4197,
Homo sapiens	ENSG00000100814	1 retrocopy	retro_hsap_4877,
Gorilla gorilla	ENSGGOG00000004586	1 retrocopy	retro_ggor_3046,
Microcebus murinus	ENSMICG00000000893	2 retrocopies	retro_mmur_1264, retro_mmur_1551,
Macaca mulatta	ENSMMUG00000016251	2 retrocopies	retro_mmul_2617, retro_mmul_371,
Nomascus leucogenys	ENSNLEG00000010636	1 retrocopy	retro_nleu_2556 ,
Pan troglodytes	ENSPTRG00000006088	1 retrocopy	retro_ptro_3249,
Rattus norvegicus	ENSRNOG00000026056	1 retrocopy	retro_rnor_842,
Ictidomys tridecemlineatus	ENSSTOG00000004394	1 retrocopy	retro_itri_1590,