RetrogeneDB ID: retro_ptro_3069

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL393505.1:1142419..1143773(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCM2
• Ensembl ID: ENSPTRG00000019156
• Aliases: None
• Description: cerebral cavernous malformation 2 [Source:HGNC Symbol;Acc:21708]

Sequence

>retro_ptro_3069
AGAAATTCCTCAAACAGAATTTCACATGGGGTATTCCATGAAGAATTCCATGAGCCTGGAATTGTCTCGCCATTTAAACG
AGTATTCCTAGAAGGTGAAAAGAGCAGAGATAAGAAATCCCATGAGAAGATGACAGACAGGCACCCTCTGCACACTGTGG
TGTTGTCATTGCCTGAGCACATCCAGCCAGACAGACTGCTAAGTGACTATATTGAGAAGGAGGTAAAGTATTTAGGTCAG
TTAACGTGCATTCTAGGATACCTGAATCCCTCAGTAGGACTGAAATCCTGCATTTCACAGACAATGCAAACAGGCCACTA
GCTTCAGGGACACTTGACTCCGGAGCACGATGCTGTGCTCAGCCTGTCTGCGTACAATGTCCAGGCTGGCCTGGAGGGGC
GGAGAGGATATCATCCTCAGGGTGCCCATCCATGACATCACCACCGTCTTCTATGTTCGGGATGACGCCACACACCTGGT
GGTCCTGAAGACAGCCCAAGACCCAGGAATCTCCCCCAGCCAGAGTCTGTGTGCGAAAAGTTCCAGAGGCCTCTGTGCAG
GCTCCCCGTCAGAGAGTGCAGTTGGGTCCGTGGAGGCTTGCTGCCTGGTCATCCTGGCTGCAGAGAGCAAGGTCGCTGCG
GAGGAACTTTGCTGTCTGTGAGGCCAGGTCTTCCAGGTTGTTTACACGGAGTCTACCATTGACTTTCTGGACAGAGCGAT
ATTTGATGGGGCATCCACCCCCACCCACCACCTGTGCCTGCACAGCGATGATTCTTCCACAAAAGTGGACTTTAAGGAGA
CTTATGAGGTGGAAGCCAGCACTTTCTGCTTTCTTGAATCCGTGGATGTGGGTGGTGCGTCACCTCACGGCAAGACCATC
AGTGAGAGTGAGCTGAGCGCCAGCGCCACTGAGCTGCTGCAGGACTCTATGTTGACACTGCGCACCAAGCTGTTGTCGCA
GGAGATCCAGCAGTTTGCAGCGCTGTTGCACGAGTACCGCAATGGGGCCTCTGTCCACGAGTTCTTCATCGACCTTCGGC
AGCTCTATGGGGACAGCCCCAAGTTCCTGCTGCTTGGTCTGAGGCCCTTCATCCCTGAGAAAGACAGCCAGAACTTTGAA
AACTTCCTGGAGACCATTGGCGTGAAGGACCGCCGCCGCATCGTCACCGACAGCTTTGGCAGGCACCAGCGGGCCCTGAG
CACCACGTCCAGTTCCACTACCAACGGGAAAAGGACCACGTGCAGCTCTGATGACCGGTCGGCGCCCTCAGAAGGGGATG
AGGGGGACGGCATAATCTCGGACATCAGCAATGACATTGAGGCACTGGGCTGCAGCATGGACCAGGACTCAGCA

Alignment

ORF - retro_ptro_3069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.62 %
• Parental protein coverage: 97.85 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QNLSKEIPQTEFHTGYSMENEPGIVSPFKRVFLKGEKSRDKKAHEKVTERRPLHTVVLSLPERVEPDRLL
          .N.S..I....FH.......EPGIVSPFKRVFL.GEKSRDKK.HEK.T.R.PLHTVVLSLPE...PDRLL
Retrocopy RNSSNRISHGVFHEEF---HEPGIVSPFKRVFLEGEKSRDKKSHEKMTDRHPLHTVVLSLPEHIQPDRLL

Parental  SDYIEKEVKYLGQLTSIPGYLNPS-SRTEILHFIDNA-KRA-HQLPGHLTQEHDAVLSLSAYNV-KLAWR
          SDYIEKEVKYLGQLT.I.GYLNPS.SRTEILHF.DNA.K.A.H.L.GHLT.EHDAVLSLSAYNV..LAWR
Retrocopy SDYIEKEVKYLGQLTCILGYLNPS<SRTEILHFTDNA<KQA<H*LQGHLTPEHDAVLSLSAYNV>RLAWR

Parental  DGEDIILRVPIHDIAAVSYVRDDAAHLVVLKTAQDPGISPSQSLCAESSRGLSAGSLSESAVGPVEACCL
          .GEDIILRVPIHDI..V.YVRDDA.HLVVLKTAQDPGISPSQSLCA.SSRGL.AGS.SESAVG.VEACCL
Retrocopy GGEDIILRVPIHDITTVFYVRDDATHLVVLKTAQDPGISPSQSLCAKSSRGLCAGSPSESAVGSVEACCL

Parental  VILAAESKVAAEELCCLLGQVFQVVYTESTIDFLDRAIFDGASTPTHHLSLHSDDSSTKVDIKETYEVEA
          VILAAESKVAAEELCCL.GQVFQVVYTESTIDFLDRAIFDGASTPTHHL.LHSDDSSTKVD.KETYEVEA
Retrocopy VILAAESKVAAEELCCL*GQVFQVVYTESTIDFLDRAIFDGASTPTHHLCLHSDDSSTKVDFKETYEVEA

Parental  STFCFPESVDVGGASPHGKTISESELSASATELLQDYMLTLRTKLSSQEIQQFAALLHEYRNGASIHEFC
          STFCF.ESVDVGGASPHGKTISESELSASATELLQD.MLTLRTKL.SQEIQQFAALLHEYRNGAS.HEF.
Retrocopy STFCFLESVDVGGASPHGKTISESELSASATELLQDSMLTLRTKLLSQEIQQFAALLHEYRNGASVHEFF

Parental  INLRQLYGDSRKFLLLGLRPFIPEKDSQHFENFLETIGVKDGRGIITDSFGRHRRALSTTSSSTTNGNRA
          I.LRQLYGDS.KFLLLGLRPFIPEKDSQ.FENFLETIGVKD.R.I.TDSFGRH.RALSTTSSSTTNG.R.
Retrocopy IDLRQLYGDSPKFLLLGLRPFIPEKDSQNFENFLETIGVKDRRRIVTDSFGRHQRALSTTSSSTTNGKRT

Parental  TGSSDDRSAPSEGDEWDRMISDISSDIEALGCSMDQDSA
          T.SSDDRSAPSEGDE.D..ISDIS.DIEALGCSMDQDSA
Retrocopy TCSSDDRSAPSEGDEGDGIISDISNDIEALGCSMDQDSA

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	105.94 RPM
SRP007412_cerebellum	0.00 RPM	50.01 RPM
SRP007412_heart	0.00 RPM	10.67 RPM
SRP007412_kidney	0.00 RPM	29.89 RPM
SRP007412_liver	0.00 RPM	57.02 RPM
SRP007412_testis	0.00 RPM	10.96 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3069 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3069 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000019156	1 retrocopy	retro_ptro_3069 ,