RetrogeneDB ID: retro_hsap_4333

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: GL000229.1:12744..14369(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC27
• Ensembl ID: ENSG00000004897
• Aliases: CDC27, ANAPC3, APC3, CDC27Hs, D0S1430E, D17S978E, HNUC, NUC2
• Description: cell division cycle 27 [Source:HGNC Symbol;Acc:1728]

Sequence

>retro_hsap_4333
ATGACGATGCTACAGGAACCCGTCCAGGTTGCTACATGGCAAGCACTAAACCACTATGCTTACCGAGATGGGGTTTTCCT
CGCAGAACGCCTTTACGCAGAAGTACACTCAGAAGAAGCCTTGTTTTTACTGGCGACCTGTTCTTACTGCCCAGGAAAGG
CCTATAAAGCATATAGACTCTTGAAAGGACACAGTTGTCCTACACCGCAATGCAAGTACCTGCTTGCAAAATGTTGTTTT
GATGTCAGCAAGCTTGCAGAAGGGGAACAAATCTTATCTGGTGGAGTGTTTCATAAGCAGAAAAGCCATGATGATATTGT
TACTGAGTTTGGTGATTCAGCTTGCTTTCCCCTTCCATTGTTGGGACATGTATATTGCAAGACAGATCGGCTTGCCAAAG
GATCAGAATGCTACCAAAAGAGCCTTAGTTTAAATCCTTTCCTCTGGTATCCCTTTGAATCATTATTTGAAATAGGTGAA
AAGCCAGATCCTGACCAAAGTTTTAAATTCACATCTTTACATAACTTTAGCAACTGTCTGTCCAAGTGTTGCACCACACA
AGTACCTCGTCATAGTTTATGTCACAGACAGCCTGAGACTGTTCTTATGGAAACACCCCAGAACGCAACTGAATTAAACA
GATTGAATTTAGAATCTTCCAATTCAAAGTACTCCTTGAATACAGATTCCCCAGTGTCTTCTATTGATTCAGCTGTAATT
TCACCTGATACTCTCCCACTGGGAACAGGAACTTCCATATTATCTAAACAGGTTCAAAATAAAGCAAAAACTGATCGAAC
TTTATTAGGAGGACCAGCATCTCTTAGTCCATTAACCCCAAGTTTTGGGATTTTACCATTAGAAACCCCAAGTCCTGGAG
ATGGATCCTATTTACAAAACTACACTAATACACCTTCTGTAATGGATATGACATCCACCGGAGTCCCTTCAAAAAAGTCT
GTTGCCAGAATAGGCCAAATTGGAGCAAAGTCTGTCTTCTCACAGAGTGGAAATAGCCGAGAGGTAACTCCAATTCTTGC
ACAAACAGAAAGTTCTGGTCCATAAATAAGTACAACACCTCAGGTATTGAGCCACACTATGATATCTCCCCCAAATGCAC
TGCATTGAAGAAGTTCACGACTCTTTACTCGTGACAGTTCCACAACCAAGGAGAATAGGAAGAAATTAAAAATGAAGTTT
CCACCTAAAATCCCAAACAGAAAAACAAAAAGTAAAACTAATAAAGGAGTAATAACTCAACCTAATATAAATGACAGCCT
GGAAACAACAAAATTGGACTCTTCCATCATTTCAGAAGGGAAAATATCCACAATCACACCTCAGATTCAGGCTTTTAGTC
TACAAAAAGCAGCAGCAGAAGACTTGATGAGCCTTCTTCGTGAAAGGGGGAAGGTTATTTAGCTTTGTGTTCATACCACT
GCAAAGAAGCTATAAATATTTTGAGCCATTTACCTTCTCACCACTACAATACTGGTTGGGTACTGTGCCAAATTGGAAGG
GCCTATTTTGAACTTTCAGAGTCCATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGTCGAAG
CCATGGAAATCTACTCTACAACACT

Alignment

ORF - retro_hsap_4333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.03 %
• Parental protein coverage: 65.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTVLQEPVQAAIWQALNHYAYRDAVFLAERLYAEVHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQ
          MT.LQEPVQ.A.WQALNHYAYRD.VFLAERLYAEVHSEEALFLLATC.Y..GKAYKAYRLLKGHSC.TPQ
Retrocopy MTMLQEPVQVATWQALNHYAYRDGVFLAERLYAEVHSEEALFLLATCSYCPGKAYKAYRLLKGHSCPTPQ

Parental  CKYLLAKCCVDLSKLAEGEQILSGGVFNKQKSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQK
          CKYLLAKCC.D.SKLAEGEQILSGGVF.KQKSHDDIVTEFGDSACF.L.LLGHVYCKTDRLAKGSECYQK
Retrocopy CKYLLAKCCFDVSKLAEGEQILSGGVFHKQKSHDDIVTEFGDSACFPLPLLGHVYCKTDRLAKGSECYQK

Parental  SLSLNPFLWSPFESLCEIGEKPDPDQTFKFTSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTI
          SLSLNPFLW.PFESL.EIGEKPDPDQ.FKFTSL.NFSNCL...CTTQVP.HSL.HRQPETVL.ETPQ...
Retrocopy SLSLNPFLWYPFESLFEIGEKPDPDQSFKFTSLHNFSNCLSKCCTTQVPRHSLCHRQPETVLMETPQNAT

Parental  ELNRLNLESSNSKYSLNTDSSVSYIDSAVISPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTP
          ELNRLNLESSNSKYSLNTDS.VS.IDSAVISPDT.PLGTGTSILSKQVQNK.KT.R.LLGGPA.LSPLTP
Retrocopy ELNRLNLESSNSKYSLNTDSPVSSIDSAVISPDTLPLGTGTSILSKQVQNKAKTDRTLLGGPASLSPLTP

Parental  SFGILPLETPSPGDGSYLQNYTNTPPVIDVPSTGAPSKKSVARIGQTGTKSVFSQSGNSREVTPILAQTQ
          SFGILPLETPSPGDGSYLQNYTNTP.V.D..STG.PSKKSVARIGQ.G.KSVFSQSGNSREVTPILAQT.
Retrocopy SFGILPLETPSPGDGSYLQNYTNTPSVMDMTSTGVPSKKSVARIGQIGAKSVFSQSGNSREVTPILAQTE

Parental  SSGPQTSTTPQVLSPTITSPPNALPRRSSRLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQ
          SSGP..STTPQVLS.T..SPPNAL..RSSRLFT.DSSTTKEN.KKLKMKFPPKIPNRKTKSKTNKG.ITQ
Retrocopy SSGP*ISTTPQVLSHTMISPPNALH*RSSRLFTRDSSTTKENRKKLKMKFPPKIPNRKTKSKTNKGVITQ

Parental  PNINDSLEITKLDSSIISEGKISTITPQIQAFNLQKAAAEGLMSLLREMGK-GYLALCSYNCKEAINILS
          PNINDSLE.TKLDSSIISEGKISTITPQIQAF.LQKAAAE.LMSLLRE.GK.GYLALCSY.CKEAINILS
Retrocopy PNINDSLETTKLDSSIISEGKISTITPQIQAFSLQKAAAEDLMSLLRERGK<GYLALCSYHCKEAINILS

Parental  HLPSHHYNTGWVLCQIGRAYFELSEYMQAERIFSEVRRIENY-RVEGMEIYST
          HLPSHHYNTGWVLCQIGRAYFELSE.MQAERIFSEVRRIENY.R..G...Y.T
Retrocopy HLPSHHYNTGWVLCQIGRAYFELSESMQAERIFSEVRRIENYSRSHGNLLYNT

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
bodymap2_adipose	0.00 RPM	102.31 RPM
bodymap2_adrenal	0.00 RPM	80.75 RPM
bodymap2_brain	0.00 RPM	93.64 RPM
bodymap2_breast	0.02 RPM	82.34 RPM
bodymap2_colon	0.00 RPM	52.32 RPM
bodymap2_heart	0.00 RPM	61.75 RPM
bodymap2_kidney	0.00 RPM	60.10 RPM
bodymap2_liver	0.00 RPM	39.40 RPM
bodymap2_lung	0.00 RPM	62.99 RPM
bodymap2_lymph_node	0.00 RPM	48.46 RPM
bodymap2_ovary	0.00 RPM	80.27 RPM
bodymap2_prostate	0.00 RPM	72.93 RPM
bodymap2_skeletal_muscle	0.00 RPM	66.46 RPM
bodymap2_testis	0.00 RPM	100.28 RPM
bodymap2_thyroid	0.00 RPM	127.28 RPM
bodymap2_white_blood_cells	0.00 RPM	78.50 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4333 was not detected

EST

No EST(s) were mapped for retro_hsap_4333 retrocopy.

TSS

No TSS is located nearby retro_hsap_4333 retrocopy 5' end.

Lab

retro_hsap_4333 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4333 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,