RetrogeneDB ID: retro_ptro_1852

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:190840100..190840632(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPS2
• Ensembl ID: ENSPTRG00000023046
• Aliases: None
• Description: None

Sequence

>retro_ptro_1852
TCACCAGAGGAGACCGAAGGAACAAATTTTGACTTTGCAGGAGAAGCTGTGGGCCAGGCAGAAAGAAAAGGACCAGCTTT
TTCTGCAGCTGAAGAAAGTTTCCATGAGGAAGAAAAACGGAGGCGAAAGGAGCAGAGCGACCTGACCTTCTGACATCCGC
TGTGAGCCGGCGGAGCCCGATTATTCACGTGGGGACTCGCTTCCTCCTCGGCATGCAGGCAGCGCTGGAGGGCACGATAG
CCCGGGCATTGTCATAGCAGCTGACCCAGCCAAGCAGATGTTCAGACCCCACGTGCTTACGACCCGGAAGTCCGTGGGCT
CAGCGGCGGCTTTTGCAGGGACCCCAGAGCAGGCAGCCTGGGCGGTGCCGCTGGGACTGCTCAGCCCCTACCTCAATATG
GGCCCACATAGCTAGCCTATGGCCCTAGTCGGCAGCTCAGAGCAGTTCAGTGCTCCCTGGGGTGCATTCATGTCCCAGCC
ACAACCTTATGTTCTGCTGGGCCACTTTCAGCACACCCAGACAGGGTTCCTC

Alignment

ORF - retro_ptro_1852 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.1 %
• Parental protein coverage: 56.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  SLEET-KEQILKLEEKLLALQEEKHQLFLQLKKV-LHEEEKRRRKEQSDLT-TLTSAAYQQSLTVHTGTH
          S.EET.KEQIL.L.EKL.A.Q.EK.QLFLQLKKV..HEEEKRRRKEQSDLT..LTSA....S...H.GT.
Retrocopy SPEET>KEQILTLQEKLWARQKEKDQLFLQLKKV<FHEEEKRRRKEQSDLT<LLTSAVSRRSPIIHVGTR

Parental  -LLSMQ-GSPGGHNRPGTLMAADRAKQMFGPQVLTTRHYVGSAAAFAGTPEH-GQFQGSPGGAYGTAQPP
          .LL.MQ.GS.GGH..PG...AAD.AKQMF.P.VLTTR..VGSAAAFAGTPE..G...G..G....TAQP.
Retrocopy FLLGMQ<GSAGGHDSPGIVIAADPAKQMFRPHVLTTRKSVGSAAAFAGTPEQ<GSLGGAAG----TAQPL

Parental  PHYGPTQPAYSPSQQLRA-PSAFPAVQ-YLSQPQPQPYAVHGHFQPTQTGFL
          P.YGPT..AY.PS.QLRA..S..P.V....SQ..PQPY...GHFQ.TQTGFL
Retrocopy PQYGPT*LAYGPSRQLRA<SSVLPGVH<FMSQ--PQPYVLLGHFQHTQTGFL

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	0.23 RPM	45.13 RPM
SRP007412_cerebellum	0.04 RPM	44.31 RPM
SRP007412_heart	0.00 RPM	29.09 RPM
SRP007412_kidney	0.03 RPM	68.70 RPM
SRP007412_liver	0.00 RPM	45.96 RPM
SRP007412_testis	1.37 RPM	224.47 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1852 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1852 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1852 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2738
Gorilla gorilla	retro_ggor_1907
Macaca mulatta	retro_mmul_1487

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016576	2 retrocopies	retro_amel_1236, retro_amel_362,
Equus caballus	ENSECAG00000010635	2 retrocopies	retro_ecab_124, retro_ecab_480,
Homo sapiens	ENSG00000132522	2 retrocopies	retro_hsap_2738, retro_hsap_4222,
Gorilla gorilla	ENSGGOG00000001672	1 retrocopy	retro_ggor_1907,
Macropus eugenii	ENSMEUG00000010645	2 retrocopies	retro_meug_1327, retro_meug_182,
Myotis lucifugus	ENSMLUG00000026169	1 retrocopy	retro_mluc_1045,
Mus musculus	ENSMUSG00000023170	1 retrocopy	retro_mmus_1476,
Nomascus leucogenys	ENSNLEG00000009364	2 retrocopies	retro_nleu_2477, retro_nleu_600,
Pan troglodytes	ENSPTRG00000023046	1 retrocopy	retro_ptro_1852 ,
Pteropus vampyrus	ENSPVAG00000005052	1 retrocopy	retro_pvam_35,
Sus scrofa	ENSSSCG00000017940	1 retrocopy	retro_sscr_742,