RetrogeneDB ID: retro_pabe_3798

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:100548750..100550379(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRKCI
• Ensembl ID: ENSPPYG00000014289
• Aliases: None
• Description: protein kinase C iota type [Source:RefSeq peptide;Acc:NP_001126946]

Sequence

>retro_pabe_3798
GAGACGTGTTCTTTTGACAACGAACAGCTCTTCACCATGAAATGGATAGACGAGGAAGGAGACCCGTGTACAGTATCATC
TCAGTTGGAGTTAGAAGAAGCCTTTAGACTTTATAAGCTAAACAAGGACTCTGAACTGTTGATTCATGTGTTCCCTTGTG
TACCAGAACGTCCCGGGATGCCTTGTCCAAGAGAAGATAAATCCATCTACCATAGAGGTGCATGCCGCTGGAGAAAGCTT
TATTGTGCCAATGGCCACACTTTCCAAGCCAAGCGCTTCAACAGGCGTGCTCACTGTGCCATCTGCACAGACCGAATATG
GGGACTTGGACGCCAAGGATATAAGTGCATCAACTTCAAACTCTTGGTTCATAAGAAGTGCCATAAACGCCTCACAATTG
AATGTGGGCGGCATTCTTTGCCACTGGAACAAATGATGCCCATGGATCAGTCATCCATGCATTCTGACCATGCACAGACA
GTAATTCCATATAATCCTTCAAGTCATGAGAGTTTGGATCAAGTTGGTGAAGAAAAAGAGGCAATGAACACCAGGGAAAG
TGGCAAAGCTTCATCCAGTCTAGGTCTTCAGGATTTTGATTTGCTCCGGGTAATAGGAAGAGGAAGTTAAGCCAAAGTAC
TGTTGGTTCCATTAAAAAAAAAAAAAAAGATCGTATTTATGCAATGAAAGTTGTGAAAAAAGAGCTTGTTAATGATGATG
AGGATATTGATTGGGTGCAGACAGAGACATATGTGTTTGAGTAGGCATCCAATCATCCTTTCCTTGTTGGGCTGCAGTGT
TGCTTTCAGACAGAAAGTAGATTGTTCTTTGTTATAGAGTATATAAATGGAGGAGACCTAATGTTTCATATGCAGCGACA
AAGAAAATTTCCTGAAGAACATGCCAGATTTTACTCTGCAGAAATCAGTCTAGCATTCAATTATCTTCATGAGCGAGGGA
TAATTTATAGAGATTTGAAACTGGACAATGTACTACTGGACTCTGAAGGCCACATTAAACTCACTGACTACGGCATGTGT
TAAGGAAGGATTACGGCCAGGAGATACAACCAGCACTTTCTGTGGTACTCCTAATTACATTGCTCCTGAAATTTTAAGAG
GAGGAGATTATGGTTTCAGTGTTGACTGGTGGGCTCTTGGAGTGCTAATGTTTGAGATGATGGCAGGAAAGTCTCCATTT
GATACTGTTGGGAGCTCCGATAACCCTGACCAGAACACAGAGGATTATCTCTTCCAAGTTATTTTGGAAAAACAAATTCG
CATACCACGTTCTCTGTCTGTAAAAGCTGCAAGTGTTCTGAAGAGTTTTCTTAACAAGGACCCTAAGGAATGATTGGGTT
GTCATCCTCAAACAGGATTTGCTGATATTCAGGGACACCCGTTCTTCTGAAATGTTGATTGGGATATGATGGAGCAAAAA
CAGGTAGTACTTCCCTTTAAAGCAAATATTTCTGGGGAATTTGGTTTGGACAACTTTGATTCTCAGCTTACTAATGAACC
TGTCCAGCTCACTCCAGATGTCGATGACATTGTGAGGAAGATTAATCAGTCTGAATTTGAAGGTTTTGAGTATATCAATC
CTCTTTTGATGTCTGCAGAAGAATGTGTC

Alignment

ORF - retro_pabe_3798 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.38 %
• Parental protein coverage: 78.41 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DMCSFDNEQLFTMKWIYDEGDPCTVSSQLELEEAFRLYELNKDSELLIHVFPCVPERPGMPCPGEDKSIY
          ..CSFDNEQLFTMKWI..EGDPCTVSSQLELEEAFRLY.LNKDSELLIHVFPCVPERPGMPCP.EDKSIY
Retrocopy ETCSFDNEQLFTMKWIDEEGDPCTVSSQLELEEAFRLYKLNKDSELLIHVFPCVPERPGMPCPREDKSIY

Parental  RRGARRWRKLYCANGHTFQAKRFNRRAHCAICTDRIWGLGRQGYKCINCKLLVHKKCHKLVTIECGRHSL
          .RGA.RWRKLYCANGHTFQAKRFNRRAHCAICTDRIWGLGRQGYKCIN.KLLVHKKCHK..TIECGRHSL
Retrocopy HRGACRWRKLYCANGHTFQAKRFNRRAHCAICTDRIWGLGRQGYKCINFKLLVHKKCHKRLTIECGRHSL

Parental  PPEPMMPMDQSSMHSDHAQTVIPYNPSSHESLDQVGEEKEAMNTRESGKASSSLGLQDFDLLRVIGRGSY
          P.E.MMPMDQSSMHSDHAQTVIPYNPSSHESLDQVGEEKEAMNTRESGKASSSLGLQDFDLLRVIGRGS.
Retrocopy PLEQMMPMDQSSMHSDHAQTVIPYNPSSHESLDQVGEEKEAMNTRESGKASSSLGLQDFDLLRVIGRGS*

Parental  AKVLLVRLKKTDRIYAM--KVVKK-ELVNDDEDIDWVQTEKHVFEQASNHPFLVGLHSCFQTESRLFFVI
          AKVLLV.......I..M..K..KK.ELVNDDEDIDWVQTE..VFE.ASNHPFLVGL..CFQTESRLFFVI
Retrocopy AKVLLVPXXXXXXIVFMQ*KL*KK<ELVNDDEDIDWVQTETYVFE*ASNHPFLVGLQCCFQTESRLFFVI

Parental  EYVNGGDLMFHMQRQRKLPEEHARFYSAEISLALNYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMC-K
          EY.NGGDLMFHMQRQRK.PEEHARFYSAEISLA.NYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMC.K
Retrocopy EYINGGDLMFHMQRQRKFPEEHARFYSAEISLAFNYLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMC>K

Parental  EGLRPGDTTSTFCGTPNYIAPEILRGEDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNPDQNTEDYLF
          EGLRPGDTTSTFCGTPNYIAPEILRG.DYGFSVDWWALGVLMFEMMAG.SPFD.VGSSDNPDQNTEDYLF
Retrocopy EGLRPGDTTSTFCGTPNYIAPEILRGGDYGFSVDWWALGVLMFEMMAGKSPFDTVGSSDNPDQNTEDYLF

Parental  QVILEKQIRIPRSLSVKAASVLKSFLNKDPKERLGCHPQTGFADIQGHPFFRNVDWDMMEQKQVVPPFKP
          QVILEKQIRIPRSLSVKAASVLKSFLNKDPKE.LGCHPQTGFADIQGHPFF.NVDWDMMEQKQVV.PFK.
Retrocopy QVILEKQIRIPRSLSVKAASVLKSFLNKDPKE*LGCHPQTGFADIQGHPFF*NVDWDMMEQKQVVLPFKA

Parental  NISGEFGLDNFDSQFTNEPVQLTPDDDDIVRKIDQSEFEGFEYINPLLMSAEECV
          NISGEFGLDNFDSQ.TNEPVQLTPD.DDIVRKI.QSEFEGFEYINPLLMSAEECV
Retrocopy NISGEFGLDNFDSQLTNEPVQLTPDVDDIVRKINQSEFEGFEYINPLLMSAEECV

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	0.39 RPM	22.95 RPM
SRP007412_cerebellum	0.00 RPM	20.06 RPM
SRP007412_heart	0.09 RPM	5.66 RPM
SRP007412_kidney	0.17 RPM	12.50 RPM
SRP007412_liver	0.00 RPM	4.77 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3798 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3798 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3798 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4884
Pan troglodytes	retro_ptro_3254

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000015212	1 retrocopy	retro_cpor_656,
Homo sapiens	ENSG00000163558	1 retrocopy	retro_hsap_4884,
Pongo abelii	ENSPPYG00000014289	1 retrocopy	retro_pabe_3798 ,
Pan troglodytes	ENSPTRG00000015615	1 retrocopy	retro_ptro_3254,