RetrogeneDB ID: retro_ptro_996

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:24521823..24522421(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPTRG00000008796
• Aliases: None
• Description: None

Sequence

>retro_ptro_996
ATGTTGCATCAGTACAGTAATGATGACACTGAAGACATTTCAGTGTTGGATGTGGAAGAGACAACTAACAAAACAAAACA
ATCCAAAATCAGATATCCAGTGGCCTCACGTTTCCAGCTATTCTTTCAAGTCAGTGCAATTGTGGTCTACCTTCTTTGCA
AATTGGTCAGCAGCAGCTTTACTGCTTGTATGGTGACAACTATCTCGTCATGTGACTTTAGGGCAGTGACGAATGTCACA
GGTAGACTAGTGGTGGGTCTACGGTGTTGGAATCACATGATGAAGATGGAAAGAGCCATTGGGTGCTTGAGTCCAGAAAG
GCATCCTCTCGGGAGGACAAAACTGTCTCAGAGGCTGAATCAAATCTTTTGGTTGTGACTTAATGCCTGTCCAGTGCTGT
GGGTGATATTTATCTTTAGTGGCCTCTTCTCCTTCAGGGTAAAGTGGTTAGCAGTGGTTATCATGGGTGTGGTGCTACAA
GGTGCCAACCTATATGGCTACATCAGGTGTAAATAGGCAACGGAAAGAATGTAACCAGCATGGGTCCCTCATACTTGGAA
AGCAGTTTTTAAGACAAAACACTGAGGATGATCAGACT

Alignment

ORF - retro_ptro_996 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.05 %
• Parental protein coverage: 99.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VLQQDSNDDTEDVSLFDAEEETTNRPRKAKIRHPVASFFHLFFRVSAIIVCLLCELLSSSFITCMVTIIL
          .L.Q.SNDDTED.S..D.EE.TTN.....KIR.PVAS.F.LFF.VSAI.V.LLC.L.SSSF..CMVT.I.
Retrocopy MLHQYSNDDTEDISVLDVEE-TTNKTKQSKIRYPVASRFQLFFQVSAIVVYLLCKLVSSSFTACMVTTIS

Parental  LLSCDFWAVKNVTGRLMVGLRWWNHI-DEDGKSHWVFESRKESSENKT-VSEAESRIFWLGLIACSVLWV
          ..SCDF.AV.NVTGRL.VGLR.WNH..DEDGKSHWV.ESRK.SS......S.....IFWL.L.AC.VLWV
Retrocopy --SCDFRAVTNVTGRLVVGLRCWNHM<DEDGKSHWVLESRKASSREDK>LSQRLNQIFWL*LNACPVLWV

Parental  IFAFSALFSFRVKWLAVVIMGVVLQGANLYGYIRCK-VRSRKNLTSMVTSY-FGKQFLRQNTGDDQT
          IF.FS.LFSFRVKWLAVVIMGVVLQGANLYGYIRCK.....KN.TSM..SY..GKQFLRQNT.DDQT
Retrocopy IFIFSGLFSFRVKWLAVVIMGVVLQGANLYGYIRCK<IGNGKNVTSMGPSY<LGKQFLRQNTEDDQT

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	0.02 RPM	1.84 RPM
SRP007412_cerebellum	0.00 RPM	1.47 RPM
SRP007412_heart	0.00 RPM	0.70 RPM
SRP007412_kidney	0.00 RPM	1.44 RPM
SRP007412_liver	0.00 RPM	0.56 RPM
SRP007412_testis	0.00 RPM	1.16 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_996 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_996 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_996 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_2125

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Homo sapiens	ENSG00000171928	1 retrocopy	retro_hsap_2278,
Homo sapiens	ENSG00000175106	1 retrocopy	retro_hsap_1625,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Microcebus murinus	ENSMICG00000015098	4 retrocopies	retro_mmur_1331, retro_mmur_151, retro_mmur_161, retro_mmur_683,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978,
Pan troglodytes	ENSPTRG00000007790	1 retrocopy	retro_ptro_20,
Pan troglodytes	ENSPTRG00000008796	1 retrocopy	retro_ptro_996 ,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000, retro_tsyr_530,