RetrogeneDB ID: retro_ptro_80

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:67564677..67565733(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000021003
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PRKACA
• Ensembl ID: ENSPTRG00000010585
• Aliases: None
• Description: protein kinase, cAMP-dependent, catalytic, alpha [Source:HGNC Symbol;Acc:9380]

Sequence

>retro_ptro_80
ATGGGCAACGCCCCCGCCAAGAAGGACACCGAGCAGGAGGAGAGCGTGAACGAGTTCCTAGCCAAAGCCAGAGGAGATTT
CCTCTACAGATGGGGAAACCCCGCTCAAAACACCGCCAGCTCGGATCAGTTCGAACGGCTCAGGACGCTGGGCATGGGCT
CCTTCGGGCGGGTGATGCTGGTGAGGCACCGGGAGACCGGCGGCCACTACGCCATGAAGATCCTCAACAAGCAGAAGGTG
GTGAAGATGAAGCAGGTCGAGCATATACTGAACGAGAAGCGCATCCTGCAGGCGATCGACTTTCCGTTCCTCGTCAAACT
CCAGTTCTCCTTTAAGGACAACTCCTACCTGTACCTGGTGATGGAGTACGTGCCCGGTGGGGAGATGTTCTCCCGCCTAC
AGCGCGTCGGAAGGTTTAGCGAGCCCCATGCCTGTTTCTATGCCGCCCAGGTCGTCCTGGCCTTCCAGTACCTACACTCG
CTCGACCTCATCCACCGCGACCTGAAGCCAGAGAATCTCCTCATCGACCAGCAGGGCTACCTGCAGGTGACGGACTTCGG
TTTCGCCAAGCGCGTGAAGGGCCGCACTTGGACCTTGTGCGGGACCCCAGAGTACCTGGCCCCCGAGATCATCCTGAGCA
AAGGCTACAACAAGGCCGTGGACTGGTGGGCCCTAGGGGTGCTCATCTATGAGATGGCCGTGGGCTTCTCACCCTTCTAC
GCCGACCAGCCCATCCAGATCTACGAGAAGATCGTCTCTGGGAGGGTGCGGTTTCCCTCCAAACTCAGCTCTGACCTCAA
GGATCTGCTGCGGAGCCTGCTGCAGGTGGACCTCACCAAGCGCTTCGGAAACCTCAGGAACGGGGTTGGCGACATCAAGA
ACCACAAGTGGTTCGCCACAACCAGCTGGATCGCCATCTATGAGAAGAAGGTGGAAGCTCCCTTCATCCCGAAGTACACA
GGCCCTGGGGATGCCAGTAACTTTGACGACTACGAGGAGGAGGAGCTCCGGATCTCCATCAATGAGAAGTGTGCCAAGGA
GTTTTCTGAGTTTTAG

Alignment

ORF - retro_ptro_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.52 %
• Parental protein coverage: 97.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKEFLAKAKEDFLKKWESPAQNTAHLDQFERIKTLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQ
          V.EFLAKA..DFL..W..PAQNTA..DQFER..TLG.GSFGRVMLV.H.ETG.HYAMKIL.KQKVVK.KQ
Retrocopy VNEFLAKARGDFLYRWGNPAQNTASSDQFERLRTLGMGSFGRVMLVRHRETGGHYAMKILNKQKVVKMKQ

Parental  IEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGEMFSHLRRIGRFSEPHARFYAAQIVLTF
          .EH.LNEKRILQA..FPFLVKL.FSFKDNS.LY.VMEYVPGGEMFS.L.R.GRFSEPHA.FYAAQ.VL.F
Retrocopy VEHILNEKRILQAIDFPFLVKLQFSFKDNSYLYLVMEYVPGGEMFSRLQRVGRFSEPHACFYAAQVVLAF

Parental  EYLHSLDLIYRDLKPENLLIDQQGYIQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWAL
          .YLHSLDLI.RDLKPENLLIDQQGY.QVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWAL
Retrocopy QYLHSLDLIHRDLKPENLLIDQQGYLQVTDFGFAKRVKGRTWTLCGTPEYLAPEIILSKGYNKAVDWWAL

Parental  GVLIYEMAAGYPPFFADQPIQIYEKIVSGKVRFPSHFSSDLKDLLRNLLQVDLTKRFGNLKNGVNDIKNH
          GVLIYEMA.G..PF.ADQPIQIYEKIVSG.VRFPS..SSDLKDLLR.LLQVDLTKRFGNL.NGV.DIKNH
Retrocopy GVLIYEMAVGFSPFYADQPIQIYEKIVSGRVRFPSKLSSDLKDLLRSLLQVDLTKRFGNLRNGVGDIKNH

Parental  KWFATTDWIAIYQRKVEAPFIPKFKGPGDTSNFDDYEEEEIRVSINEKCGKEFSEF
          KWFATT.WIAIY..KVEAPFIPK..GPGD.SNFDDYEEEE.R.SINEKC.KEFSEF
Retrocopy KWFATTSWIAIYEKKVEAPFIPKYTGPGDASNFDDYEEEELRISINEKCAKEFSEF

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	52.66 RPM
SRP007412_cerebellum	0.04 RPM	95.39 RPM
SRP007412_heart	0.03 RPM	113.84 RPM
SRP007412_kidney	0.00 RPM	44.54 RPM
SRP007412_liver	0.03 RPM	75.65 RPM
SRP007412_testis	30.98 RPM	89.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_80 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_80 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_80 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_46
Gorilla gorilla	retro_ggor_2856
Pongo abelii	retro_pabe_61
Macaca mulatta	retro_mmul_186

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000072062	1 retrocopy	retro_hsap_46,
Gorilla gorilla	ENSGGOG00000013294	1 retrocopy	retro_ggor_2856,
Macropus eugenii	ENSMEUG00000002017	2 retrocopies	retro_meug_10, retro_meug_1166,
Monodelphis domestica	ENSMODG00000012087	1 retrocopy	retro_mdom_1978,
Pan troglodytes	ENSPTRG00000010585	1 retrocopy	retro_ptro_80 ,
Sarcophilus harrisii	ENSSHAG00000009246	2 retrocopies	retro_shar_13, retro_shar_49,