RetrogeneDB ID: retro_ptro_2503

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:170111727..170113775(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTAGE5
• Ensembl ID: ENSPTRG00000006297
• Aliases: None
• Description: None

Sequence

>retro_ptro_2503
GAGAAGGGGGCAGCAGAGGCACAAAGTTTGCAGGCAACCTGTGAAAAGCTGAACAGGTCAATTCTGAGCTTGAGCATGAA
ATACTCTGTCTAGAAAAAGAGTTAAAAGAAGAGAAATCTAAACATTCTGAACGAGATGAACTGATAGCAGATATTTCCAA
ACGGATACATTTGCTGGAAGATGAGTCAAAATCCCTCAAATCACAAATAGCTAAAGCCAAAATGACCTTCAAGACATTTC
ACATGAACGGAGAACAACTGAAGATAACAATAAAAGATGCTTTGAATGAAAATTCTCAACTTCAGGAAAACCAGAAACAG
CTTTTGCAAGAAGCTGAAGTATGGAAAGAAGAAGTGAGTGAACTTAATAAACAGAAAAGAACATTTGAAGACTCCAAAGT
ACACACAGAACAAGTTCTAAATGATAAAGAAAATCGCATCGAGACTCTGACCGAACACTTGCTAAAGATGAAAGATCGGG
CTGCGAGGCTTAGAGAAGACATAACGTATGATGGTAACTTAGAAGTGAACAGTGAATCGGAAGATGGTGCTCACTTAGAT
GATCCCTCCAAAGGAGCTTTGAAGAAGCTGATTCATGCTGCTAAGTTAAATGCTTCTTTAAAATCTTAGAAGGAGAAAGA
AACCAAATTTATATTCAGTTATCTGAAGTTGATAAAACAAAGGAAGAGCTTACAGAGCATATTAAAAATCTTCAGACTGA
ACAAGCATCTTTGCAGTTAGAAAACACACATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAAGTAATAACTG
AATTATATAAAGAAAATGAAATGAAACTCTACAGGAAATTAATAGTAGAGGAAAATTACCAGTTAGAGAAAGAAGAGAAA
CTTTCTAAAGTAGACTAAATGGGCAGCCATGCCACTAAAGAGCTGGAGACCTACAGACAGCGAGCCAAAGATCTTGAAAA
ATTTGAGAGAACTATTCATTTTTATCAAAGGAAGATTATTTCCCATGAGAAAAAGGCACATCATAACTGGTTGGCAGCTT
AGGCTGCTGAAAGAAACCTCGACGATTTAAGGAAAGAAAATGCTCACAACCGACAAAAATTAGCTGAAACAGAGTATAAA
ATAAAACTTCTAAAAAAAGATCCTTATGCACTTGATGTTCCAAATACGGCATTTGGCAGAGAGCATTCCCCATATGGTCC
CTCACCATTGGGTCGGCCTTCACCTGAAACGAGAGCTTTTCTCTATCCTCCAACTCTGTGGAAGGGTCCACTCAGACTCT
CACCTTTGCCTCCAGGGGGAGAAGGAAGAGGCTCAAGAGGCCCAGGGAATCCTCCGGACCATCAGATTACCAATGAAAGA
GGAGAATCAAGCTGTGATAGGTTAACCGATCCTCACAGGGTTCCTTCTGACACTGGGTCCCTGTCACCTCCATGGGAACA
GGACCATAGGATGATGTTTCCTCCACCAGGACCATCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTT
ACTCTAACTCTGGTAGACTGTCTGGACCAGCAGAAATCAGAAGTTTTAATATGGCTCCTTTGGATAAAATGGATGGGTCA
ATGCCTTCAGAAATGGAATCCAGTAGAAATGACACCAAAGATGATCTTGGTCATTTAAATGTGCCTGATTCATCTCTCCC
CGCTGAAAATGAAGCAGCTGGCCCCAGCTTTGTTCCTCCACCTCTTGCCCCAATCAGAGGTCCACTGTTTCCAGTGGATA
CGAGGGGCCCGTTCACGAGAAGAGGACCTGCTTTCCCCCCACCTCCTCCAGGAACCATGTTGGGAGCTTCTCGAGATTAT
TTTCCACCAGGAGATTTCCCAGGTCCACCACATGCTCTGTTTGCAATGAGAAATGTCTATCCACCGAGGGGTTTTCCTCC
TTACCCTCCCCCAAGACCTGGATTTTTCCCCCCACCCCCACATTCTAAGGTTGAAGTGAGTTCCCTTCAGGGCTGAGTCC
GCCTTCAGATGAGCCTGCTACGGAACATCAGAACCACAGCAAGAAACC

Alignment

ORF - retro_ptro_2503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.53 %
• Parental protein coverage: 85.45 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EKEATEAQSLEATCEKLNRS-NSELEDEILCLEKELKEEKSKHSERDELMADISKRIQSLEDESKSLKSQ
          EK.A.EAQSL.ATCEKLNRS.NSELE.EILCLEKELKEEKSKHSERDEL.ADISKRI..LEDESKSLKSQ
Retrocopy EKGAAEAQSLQATCEKLNRS<NSELEHEILCLEKELKEEKSKHSERDELIADISKRIHLLEDESKSLKSQ

Parental  VAEAKMTFKIFQMNEERLKIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVTFEDSEVHAEQV
          .A.AKMTFK.F.MN.E.LKI.IKDALNENSQLQE.QKQLLQEAEVWKE.VSELNKQK.TFEDS.VH.EQV
Retrocopy IAKAKMTFKTFHMNGEQLKITIKDALNENSQLQENQKQLLQEAEVWKEEVSELNKQKRTFEDSKVHTEQV

Parental  LNDKESHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASL
          LNDKE..I.TLTE.LLKMKD.AA.L.EDIT.D.NLE...NSESE.GA.LD.P.KGALKKLIHAAKLNASL
Retrocopy LNDKENRIETLTEHLLKMKDRAARLREDITYDGNLEV--NSESEDGAHLDDPSKGALKKLIHAAKLNASL

Parental  KT-LEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMK
          K..LEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQ.ENTHFE.ENQKLQQKLKV.TELY.ENEMK
Retrocopy KS<LEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQLENTHFESENQKLQQKLKVITELYKENEMK

Parental  LHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQGQIISHEKKAHDNWL
          L.RKL.VEENY.LEKEEKLSKVD...SHAT.ELETYR.RAKDLE...ERTIH.YQ..IISHEKKAH.NWL
Retrocopy LYRKLIVEENYQLEKEEKLSKVD*MGSHATKELETYRQRAKDLEK-FERTIHFYQRKIISHEKKAHHNWL

Parental  AARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFL
          AA..AERNL.DLRKENAHNRQKL.ETE.K..LL.KDPYALDVPNTAFGREHSPYGPSPLG.PS.ETRAFL
Retrocopy AA*AAERNLDDLRKENAHNRQKLAETEYKIKLLKKDPYALDVPNTAFGREHSPYGPSPLGRPSPETRAFL

Parental  SPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRM
          .PPTL..GPLRLSPL.PGG.GRGSRGPGNP.DHQITNERGESSCDRLTDPHR.PSDTGSLSPPW.QD.RM
Retrocopy YPPTLWKGPLRLSPLPPGGEGRGSRGPGNPPDHQITNERGESSCDRLTDPHRVPSDTGSLSPPWEQDHRM

Parental  MFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNV
          MFPPPG.SYPDSALPPQRQDRF.SNSGRLSGPAE.RSFNM..LDKMDGSMPSEMESSRNDTKDDLG.LNV
Retrocopy MFPPPGPSYPDSALPPQRQDRFYSNSGRLSGPAEIRSFNMAPLDKMDGSMPSEMESSRNDTKDDLGHLNV

Parental  PDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPP
          PDSSLPAENEA.GP.FVPPPLAPIRGPLFPVDTRG.F.RRGP.FPPPPPG.M.GASRDYFPP.DFPGPP.
Retrocopy PDSSLPAENEAAGPSFVPPPLAPIRGPLFPVDTRGPFTRRGPAFPPPPPGTMLGASRDYFPPGDFPGPPH

Parental  APFAMRNVYPPRGFPPYLPPRPGFFPPPPHSE-GRSEFPSGLIPPSNEPATEH-PEPQQET
          A.FAMRNVYPPRGFPPY.PPRPGFFPPPPHS..G.SEFPSGL.PPS.EPATEH..EPQQET
Retrocopy ALFAMRNVYPPRGFPPYPPPRPGFFPPPPHSK<G*SEFPSGLSPPSDEPATEH<SEPQQET

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	10.90 RPM
SRP007412_cerebellum	0.00 RPM	9.86 RPM
SRP007412_heart	0.00 RPM	11.02 RPM
SRP007412_kidney	0.08 RPM	54.97 RPM
SRP007412_liver	0.00 RPM	36.20 RPM
SRP007412_testis	7.69 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2503 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2503 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3024

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016105	4 retrocopies	retro_cjac_1747, retro_cjac_2711, retro_cjac_3217, retro_cjac_921,
Cavia porcellus	ENSCPOG00000026514	2 retrocopies	retro_cpor_189, retro_cpor_727,
Homo sapiens	ENSG00000150527	3 retrocopies	retro_hsap_1201, retro_hsap_3691, retro_hsap_640,
Homo sapiens	ENSG00000258941	1 retrocopy	retro_hsap_78,
Gorilla gorilla	ENSGGOG00000011990	1 retrocopy	retro_ggor_936,
Nomascus leucogenys	ENSNLEG00000004121	10 retrocopies	retro_nleu_1218, retro_nleu_1690, retro_nleu_2087, retro_nleu_2103, retro_nleu_2148, retro_nleu_2600, retro_nleu_2951, retro_nleu_3017, retro_nleu_3077, retro_nleu_688,
Pongo abelii	ENSPPYG00000005768	9 retrocopies	retro_pabe_1001, retro_pabe_1002, retro_pabe_1007, retro_pabe_1055, retro_pabe_1060, retro_pabe_1588, retro_pabe_2119, retro_pabe_29, retro_pabe_3024,
Pan troglodytes	ENSPTRG00000006297	10 retrocopies	retro_ptro_1286, retro_ptro_1712, retro_ptro_2503 , retro_ptro_2580, retro_ptro_2880, retro_ptro_466, retro_ptro_821, retro_ptro_826, retro_ptro_868, retro_ptro_876,
Ictidomys tridecemlineatus	ENSSTOG00000015890	1 retrocopy	retro_itri_95,