RetrogeneDB ID: retro_ptro_3068

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: GL393505.1:929337..930491(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AGGF1
• Ensembl ID: ENSPTRG00000017008
• Aliases: None
• Description: None

Sequence

>retro_ptro_3068
GAGGAAAAGGATTTGAATTCAGAGGATCAAAAAGCCTTCAGTGTTGAACATACGAGCTGAAATGGGAAAGACAATTTTAC
AAATGTGAAAGAAAGGCCAAAATAGGCATTCATCACAAAAATAATCCCCCAAAATTCACTGGTCCAGTTAGTGGAAATAC
TATGGAATCTCCTCTTAATGAAAACATCTCAATTCAACTTTATTTAAAGATGAGAAAGTCGCAGGCAGTGATAGTGAATC
AGAAGAAGGTGAAATCACAGACTCTCAGACCGAGGGTAGTTATGATGAAGACATCACCAGTGAAGGCAATGCAACTGCAA
AAGATACTGAGGAGAAAGATGAGGAATAAATGTGGCCCCCATGTATAAGAGTAATTGTCATTAGATCACCGCTGTTACAG
ACAGGATCACTCTTCATCATTACTGCTGTAAAACCTGCTACAATTGAAAGAGAAAATGATATGGAGCATACTCTTTGAAT
CCCTGCAGTTGGTGTCAGTAAGTTTCATGCACAAATTTATTTTGACCATGACTTACAAAGTTATGTCCTTTTGGATCAGG
CAGTCAAAATGGAACAATTGTTAATGAAAAACGGATTATTCAGCTGAAAACTAAATGTGACCCTTATGTACTTGAGCATG
GAGATAAAGCAAAAATTGGAGAGACTGTGTTATCTTATTATATTCACCCTGGCAGTAATAGCTGTGTTGGATGTGAACCA
GTGCAGGTTAGATCTCACCTTTCCTTGATAAGAAAGATGAATCATTTGTTGGTCCAACATTAACTAAGAAGGAAAGGAGT
TGGGAAAAAAAAGGATTTTAAAAATATATTAGTAAAATATGCTTTACAGAATACAGACTACAAAGATGATAAGATATTGG
AGAATCTAAAATATAAAGATAGAGCTGGAAAACATAGGGAACAGATTAGAAGTGAAGGAAATTTCCAAAGAGATGATGCT
CCTGCATCTGTTCATTCTGAAATTACTGATAGCAACAAAGGTCACAAGATGTTGAAGAAGATGTGTTGAAAACATTAGTA
GGCCTGGGGAAGGATGGTGGGAGAATAAAAACTCCAATACAGCTTCAACTTCGGCAAACGCAAGCAGGATTGGAGACAGA
CAAACCATCCTCAATTAAAGAGGCTCACCTTCTC

Alignment

ORF - retro_ptro_3068 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.87 %
• Parental protein coverage: 54.2 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  EEKDLNSEDQKAFSVEHTSCNEEENFANMK-KKAKIGIHHKNSPPKVTVPTSGNTIESPLHENIS-NSTS
          EEKDLNSEDQKAFSVEHTS.N...NF.N.K..KAKIGIHHKN.PPK.T.P.SGNT.ESPL.ENIS.NST.
Retrocopy EEKDLNSEDQKAFSVEHTS*NGKDNFTNVK<RKAKIGIHHKNNPPKFTGPVSGNTMESPLNENIS<NSTL

Parental  FKDEKIMETDSEPEEGEITDSQTEDSFDEDITSEGNVTAEDSEDEDEDKIWPPCIRVIVIRSPVLQIGSL
          FKDEK....DSE.EEGEITDSQTE.S.DEDITSEGN.TA.D.E..DE...WPPCIRVIVIRSP.LQ.GSL
Retrocopy FKDEKVAGSDSESEEGEITDSQTEGSYDEDITSEGNATAKDTEEKDEE*MWPPCIRVIVIRSPLLQTGSL

Parental  FIITAVNSATIGREKDMEHTLRIPEVGVSKFHAEIYFDHDLQSYVLVDQ-GSQNGTIVNGKQILQPKTKC
          FIITAV..ATI.RE.DMEHTL.IP.VGVSKFHA.IYFDHDLQSYVL.DQ.GSQNGTIVN.K.I.Q.KTKC
Retrocopy FIITAVKPATIERENDMEHTL*IPAVGVSKFHAQIYFDHDLQSYVLLDQ<GSQNGTIVNEKRIIQLKTKC

Parental  DPYVLEHGDEVKIGETVLSFHIHPGSDTCDGCEPGQVRAHLR-LDKKDESFVGPTLSKEE-KELERRKEL
          DPYVLEHGD..KIGETVLS..IHPGS..C.GCEP.QVR.HL..LDKKDESFVGPTL.K.E.KEL.....L
Retrocopy DPYVLEHGDKAKIGETVLSYYIHPGSNSCVGCEPVQVRSHLS<LDKKDESFVGPTLTKKE<KELXXXXIL

Parental  K-KIRVKYGLQNTEYEDEKTLKNPKYKDRAGKRREQVGSEGTFQRDDAPASVHSEITDSNKGRKMLEKMG
          K..I.VKY.LQNT.Y.D.K.L.N.KYKDRAGK.REQ..SEG.FQRDDAPASVHSEITDSNKG.KML.KM.
Retrocopy K<NILVKYALQNTDYKDDKILENLKYKDRAGKHREQIRSEGNFQRDDAPASVHSEITDSNKGHKMLKKMC

Parental  WKKGEGLGK-DGGGMKTPIQLQLRRTHAGLGTGKPSSIEDVHLL
          .K.....G..DGG..KTPIQLQLR.T.AGL.T.KPSSI...HLL
Retrocopy *KH**AWGR<DGGRIKTPIQLQLRQTQAGLETDKPSSIKEAHLL

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	21.74 RPM
SRP007412_cerebellum	0.00 RPM	27.57 RPM
SRP007412_heart	0.00 RPM	18.25 RPM
SRP007412_kidney	0.00 RPM	29.05 RPM
SRP007412_liver	0.00 RPM	14.63 RPM
SRP007412_testis	0.00 RPM	66.71 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_3068 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_3068 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_3068 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000015574	1 retrocopy	retro_pabe_3572,
Pan troglodytes	ENSPTRG00000017008	1 retrocopy	retro_ptro_3068 ,