RetrogeneDB ID: retro_ptro_3249

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: X:94915334..94915925(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNB1IP1
• Ensembl ID: ENSPTRG00000006088
• Aliases: None
• Description: None

Sequence

>retro_ptro_3249
CTAGATATTGTCCTCACAGAACTCAGTCCATCAGAGGAATATAAAGCTATGGTATTGGCAGGACTGCAACCAGAGATGGT
GTTGAATATTAGCGCCTGAGCACTATACTTCTGGACATATTAGGTATATCAGGAGTCTCTCTATCAAGAATACACTTTCA
ACAAAGCTGAGGGCCATCTGAAACAGATGGAGAAGATATATACTCAGCAAATACAGAGCAAAGATGTAGAATTGACCTTT
ATAAAAGGAGAGATCACCTCCATGAAGTAAGTGCTAAAAGAACACAATAAAAATGTTCACTGATATCTTTAAAAAATGTA
TGGAGTACAATCATAAGTATCAAAAAGCTCCAAAGCCTCTGTGATAGCCTGAGGCTATGAAACATTACTGTTGCTAACCA
AGAACATACCTTTGAACCATCCATAATTGCACAGTCTGGTGTTTTTGGCTTTTCATTAGGGAACAACGCCAAGTGTCTTT
TGGACAGTGTACCAGTTTAAAATTTGGGTGATGGAGATGGAGATTTTCAGTTCAGACCTTTTCTTTCTGGATTCTCACAA
AACACCTGAACCAAGCAATAGCTTTTTTTCA

Alignment

ORF - retro_ptro_3249 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.87 %
• Parental protein coverage: 70.76 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LDIVRTELSPSEEYKAMVLAGLRPEIVLDISSRALAFWTYQVHQERLYQEYNFSKAEGHLKQMEKIYTQQ
          LDIV.TELSPSEEYKAMVLAGL.PE.VL.IS..AL.FWTY.V.QE.LYQEY.F.KAEGHLKQMEKIYTQQ
Retrocopy LDIVLTELSPSEEYKAMVLAGLQPEMVLNISA*ALYFWTY*VYQESLYQEYTFNKAEGHLKQMEKIYTQQ

Parental  IQSKDVELTSMKGEVTSMKKVLEEYKKK-FSDISEKLMERNRQYQ-KLQGLYDSLRLRNITIANHEGTLE
          IQSKDVELT..KGE.TSMK.VL.E..K..F.DI..K.ME.N..YQ.KLQ.L.DSLRL.NIT.AN.E.T.E
Retrocopy IQSKDVELTFIKGEITSMK*VLKEHNKN>FTDIFKKCMEYNHKYQ>KLQSLCDSLRL*NITVANQEHTFE

Parental  PSMIAQSGVLGFPLGNNSKFPLDNTPVRNRGDGDGDFQFRP-FFVGSPTAPEPSNSFFS
          PS.IAQSGV.GF.LGNN.K..LD..PV.N.GDGDGDFQFRP.FF..S...PEPSNSFFS
Retrocopy PSIIAQSGVFGFSLGNNAKCLLDSVPV*NLGDGDGDFQFRP>FFLDSHKTPEPSNSFFS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.00 RPM	9.97 RPM
SRP007412_cerebellum	0.00 RPM	12.22 RPM
SRP007412_heart	0.00 RPM	14.31 RPM
SRP007412_kidney	0.00 RPM	14.67 RPM
SRP007412_liver	0.00 RPM	2.55 RPM
SRP007412_testis	0.00 RPM	27.08 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3249 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3249 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3249 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4877

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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,