RetrogeneDB ID: retro_ptro_1644

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:136173202..136174711(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC27
• Ensembl ID: ENSPTRG00000009326
• Aliases: None
• Description: None

Sequence

>retro_ptro_1644
ATGACGGTGCTGCAGGAACCTGTCCAGGCTGTTATATGGCAAGCACTAAACCACTATGCTTACTGAGATGGGGTTTTCCT
CGCAGAACGCCTTTATGCAGAAGTACACTCAGAAGAAGCCTTGTTTTTACAGGCGACCTGTTCTTACCGCCCAGGAAAGG
CCTATAAAGCATATAGACTCTGGAAATGACACAGTTGTCCTACACCACAATGCAAATACCTGCTTGCAAAATGTTGTGTT
GATCTTAGCAAGCTTGCAGAAGGGGAACAAATCTTATCTGGTGGAGTGTTTCATAAGCAGAAAAGCCATGATGATATTGT
TACTGAGTTTGGTGATTGAGCTTGCTTTCCCCTTCCATTGTTGGTACATGTATATTGCAAGACAGATTGGCTTGCCAAAG
GATCAGAATGTTACCAAAAGAGCCTTAGTTTAAATCCTTTCCTTTGGTATCCCTTCGAATCATTATGTGAAATAGGTGAA
AAGCCAGATCCTGACCAAACATTTAAATTCACATCTTCACAGAACTTTAGCAACTGTCTGCCCAACTCTTGCACAGCACA
AGTACCTAATCATAGTTTATGTCACAGACAGCCTGAGACCGTTCTCACGGAAACACCACAGGACTCAACTGAATTAAACA
GATTGAATTTAGAATCTTCCAATTCAAAGTACTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTATAATT
TCACCTGATACTCTCCCACTGGGAACAGGAACTTCCGTATTTTCTAAACAGGTTCAAAATAAACCAAAAACTGGTTGAAG
TTTATTAGGAGGACCAGCATCTCTTAGTCCATTAACCCCAAGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAG
ATGGATCCTATTTACAAAACTACACTAATACACCTTCTGAAATTGATGTGCCATCCACCGGATCCCCTTCAAAAAAGTCT
GTTGCCAGAATCGGCCAAACTGGAGCAAAGTCTGTCTTCTCACAGGGTGGAAATAGCCGAGAGGTAACTCCAATTCTTGC
ACAAACACAAAGTTCTGGTCCATAAATAAGTTCAACACCTCAGGTATTGAGCCCCACTATGGCATCTCCCCCAAATGTGC
TGCATTGAAGTTCACGACTCTTTACTAGTGACAGTTCCACAACCAAGGAGAATAGGAAGAAATTAAAAATGAAGTTTCCA
CCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACTCAACCTAACATAAATGATAGCCTGGA
AATTACAAAATTGGACTCTTCCATCATTTCAGAAGGGAAAATATCCACAATCACACCTCAGATTCAGGCTTTTAATCTAC
AAAAAGCAGCAGCAGAAGGCTTGATGAGCCTTTTTCGTGAAAGGGGGAAAGGTTATTTGGCTTTGTGTTCATACCACTGC
AAAGAAGCTATAAATATTTTGAGCCATTTACCTTCTCACCACTACAATACTGGTTGGGTACTGTGCCAG

Alignment

ORF - retro_ptro_1644 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.87 %
• Parental protein coverage: 61.17 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEVHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          MTVLQEPVQA.IWQALNHYAY.D.VFLAERLYAEVHSEEALFL.ATC.YR.GKAYKAYRL.K.HSC.TPQ
Retrocopy MTVLQEPVQAVIWQALNHYAY*DGVFLAERLYAEVHSEEALFLQATCSYRPGKAYKAYRLWK*HSCPTPQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLLAKCCVDLSKLAEGEQILSGGVF.KQKSHDDIVTEFGD.ACF.L.LL.HVYCKTD.LAKGSECYQK
Retrocopy CKYLLAKCCVDLSKLAEGEQILSGGVFHKQKSHDDIVTEFGD*ACFPLPLLVHVYCKTDWLAKGSECYQK

Parental  SLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTI
          SLSLNPFLW.PFESLCEIGEKPDPDQTFKFTS.QNFSNCLPNSCT.QVPNHSL.HRQPETVLTETPQD..
Retrocopy SLSLNPFLWYPFESLCEIGEKPDPDQTFKFTSSQNFSNCLPNSCTAQVPNHSLCHRQPETVLTETPQDST

Parental  ELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTP
          ELNRLNLESSNSKYSLNTDS.VS.IDSA.ISPDT.PLGTGTS..SKQVQNKPKTG.SLLGGPA.LSPLTP
Retrocopy ELNRLNLESSNSKYSLNTDSPVSSIDSAIISPDTLPLGTGTSVFSKQVQNKPKTG*SLLGGPASLSPLTP

Parental  SFGILPLETPSPGDGSYLQNYTNTPSVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQTQ
          SFGILPLETPSPGDGSYLQNYTNTPS.IDVPSTG.PSKKSVARIGQTG.KSVFSQ.GNSREVTPILAQTQ
Retrocopy SFGILPLETPSPGDGSYLQNYTNTPSEIDVPSTGSPSKKSVARIGQTGAKSVFSQGGNSREVTPILAQTQ

Parental  SSGPQTSTTPQVLSPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQ
          SSGP..S.TPQVLSPT..SPPN.L...SSRLFTSDSSTTKEN.KKLKMKFPPKIPNRKTKSKTNKGGITQ
Retrocopy SSGP*ISSTPQVLSPTMASPPNVL-H*SSRLFTSDSSTTKENRKKLKMKFPPKIPNRKTKSKTNKGGITQ

Parental  PNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSH
          PNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSL.RE.GKGYLALCSY.CKEAINILSH
Retrocopy PNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLFRERGKGYLALCSYHCKEAINILSH

Parental  LPSHHYNTGWVLCQ
          LPSHHYNTGWVLCQ
Retrocopy LPSHHYNTGWVLCQ

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	31.05 RPM
SRP007412_cerebellum	0.00 RPM	34.49 RPM
SRP007412_heart	0.06 RPM	34.54 RPM
SRP007412_kidney	0.00 RPM	25.21 RPM
SRP007412_liver	0.00 RPM	17.94 RPM
SRP007412_testis	0.53 RPM	79.56 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1644 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1644 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1644 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000004897	3 retrocopies	retro_hsap_2159, retro_hsap_4333, retro_hsap_4933,
Pongo abelii	ENSPPYG00000008945	35 retrocopies	retro_pabe_2094, retro_pabe_2169, retro_pabe_2170, retro_pabe_2172, retro_pabe_2178, retro_pabe_2182, retro_pabe_2183, retro_pabe_2184, retro_pabe_2185, retro_pabe_2186, retro_pabe_2190, retro_pabe_2192, retro_pabe_3526, retro_pabe_3545, retro_pabe_3547, retro_pabe_3550, retro_pabe_3551, retro_pabe_3553, retro_pabe_3556, retro_pabe_3582, retro_pabe_3583, retro_pabe_3589, retro_pabe_3592, retro_pabe_3598, retro_pabe_3599, retro_pabe_3603, retro_pabe_3605, retro_pabe_3606, retro_pabe_3607, retro_pabe_3609, retro_pabe_3610, retro_pabe_3827, retro_pabe_3828, retro_pabe_3833, retro_pabe_3834,
Pan troglodytes	ENSPTRG00000009326	9 retrocopies	retro_ptro_1644 , retro_ptro_2972, retro_ptro_3053, retro_ptro_3071, retro_ptro_3072, retro_ptro_3288, retro_ptro_3294, retro_ptro_3295, retro_ptro_3304,