RetrogeneDB ID: retro_ptro_826

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:58212162..58214264(+)
• 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_826
TATGAAAGCTATGAAGTAGAGTCATCTTTAGACGATTCCAGCTTTGAGAAGGAGGCAACAGAAGCACAGAGTTTGGAGGC
AACCTGTGAAAAGCTGAGCAGGTTCAATTCTGAACTGGAGCATGAAATACCCTGTCCAGAAAAGGAGTTAAAAGAAGAGA
AATCTAAACATTCTGAACAAGATGAGGTGATGGCGGATATTTCCAAAAGGATACAGTCTCTAGAAGATGAGTCAAAATCC
CTCAAATCCCATGTAGCTGAAGCCAAAATGACCTTCAAGATATTTCAAATGAATGAAGAAAGAATGAAGATAGGAATACA
GTATACTTTAAATGAAAATTCTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAAGCTGAAGTATGGAAAGAACAAG
TGAGTGAACTTAATAAACAGAAAATAACATTTGAAGACCCAAAGTACACGCAGAACAAGTTCTAAATGATAAAGAAAATC
ACATCAAGACTCTGACTGAACACTTGCTAAAGATCAAAGATCAGGCTGCTATGCTGGAAGAAGACATAACGGATGATGGT
AACTTGGAATTAGAAATGAACAGTGAATCGGAAGATGGCGCTTACTTAGATAATCCTCCAAAAGGAGCTTTGAAGAAACT
GCTTCATGCTGCTAAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGAAAGAAACCAAATTTATATACGGTTATCTAAAG
TTGATAAAACCAAGGAAGAGCTTAGAGGGCATATTAAAAATCTTCAGACAGAACAAGTATCTTTGCAGTTGGAAAACACA
CATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAGGTAATGACAGAATTATATCAAGAAAATGAAAGGAAACT
CTACAGGAAATTAATAGTAGAGGAAAATAACCGGCTAGAGAAAGAGAAACTTTCTAAAGTAGATTAAATGATCACCCATG
CCGCTGAAGAGCTGGAGACCTGCAGAAAGCAAGCCAAAGATCTTGAAGAAGAATTTCAGAGAACTACTCATATTTATCAA
GGGAAGATTATATACCATGAGAAAAAAGCACACGATAATTGTTTGGCAGCATGGACTGCTGAAAGAAACCTCGACGATTT
AAGGAAAGAAAATGCTCACAACAGACAAAAATTAGCTGAAACAGAGTTTACAATTAAACTTTTAGAAAAAGATCCTTATG
CACTTGATGTTCCAAATACAGCATTTGGCAGAGAGCATTCCTCATATGGTCCCTCACCATTGGGTCGGCCTTCATCTGAA
ATGAGAGCTTTTCTCTATCTTCCGACTTTGTTGGAGGGCCCACTGAGACTCTCACCTTTGCTTCCAGGGGGAGGAGGAAG
AGGCCCAAGAGGCCCAGGGAATCCTCTGGACCACCAGATTACCAAGGAAAGAGGAGAATCAAGCTGTGATAGGTTTACCA
ATCCTCACAGGGCTCCTTTTGACACTGGGTTCCTGTCACCTCCGTGGGAACAGGACCGTAGGATGATGTCTCCTCCACCA
GGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGGTTTTATTCTAATTGTGCTAGACGCTCTGGACC
AGCAGAACTCAGAAGTTTTAATAAGCCTCCTTTGGATAAAATGGATGGGTCAATGCCTTCAGAAATGGAATCCAGTAGAA
ATGATACCAAAGATAATCTTGGTAATTTAAATGTGCCTGATTCATCTCTCCCTGCTGGAAATGAAGTGACTGGCCCTGGC
TTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCAGTGGATACGAGGGGCCCGTTCATGAGAAGAGGACC
TCCTTTCCCTCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTTCCACCAAGGGATGTCCCAGGTCCAC
CACGTGTTCCATTTGCAATGAGAAATGTCTGTCCACTGAGGGGTTTTCCTCCTTACCTTCCCCTAAGACCTGGAATTCCC
CCCGCCACCCCCACATTCTGAAGATAGAGTGAGTTCCCTTCAGGGTTGAGTCTGCCTTCAAATGAGCCTGCTGCTGAAGA
TCCAGAACCACAGCAAGAAACC

Alignment

ORF - retro_ptro_826 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.53 %
• Parental protein coverage: 87.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  YEGYEVESSLKDASFEKEATEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSERDELMADISKR
          YE.YEVESSL.D.SFEKEATEAQSLEATCEKL.R.NSELE.EI.C.EKELKEEKSKHSE.DE.MADISKR
Retrocopy YESYEVESSLDDSSFEKEATEAQSLEATCEKLSRFNSELEHEIPCPEKELKEEKSKHSEQDEVMADISKR

Parental  IQSLEDESKSLKSQVAEAKMTFKIFQMNEERLKIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQ
          IQSLEDESKSLKS.VAEAKMTFKIFQMNEER.KI.I...LNENSQLQESQKQLLQEAEVWKEQVSELNKQ
Retrocopy IQSLEDESKSLKSHVAEAKMTFKIFQMNEERMKIGIQYTLNENSQLQESQKQLLQEAEVWKEQVSELNKQ

Parental  KVTFEDSE-VHAEQVLNDKESHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKG
          K.TFED...VHAEQVLNDKE.HIKTLTE.LLK.KD.AAML.EDITDD.NLELEMNSESE.GAYLDNPPKG
Retrocopy KITFEDPK<VHAEQVLNDKENHIKTLTEHLLKIKDQAAMLEEDITDDGNLELEMNSESEDGAYLDNPPKG

Parental  ALKKLIHAAKLNASLKTLEGERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQK
          ALKKL.HAAKLNASL.TLEGERNQIYI.LS.VDKTKEEL..HIKNLQTEQ.SLQ.ENTHFE.ENQKLQQK
Retrocopy ALKKLLHAAKLNASLTTLEGERNQIYIRLSKVDKTKEELRGHIKNLQTEQVSLQLENTHFESENQKLQQK

Parental  LKVMTELYQENEMKLHRKLTVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEELERTIHSYQG
          LKVMTELYQENE.KL.RKL.VEEN.RLEKE.KLSKVD..I.HA.EELET.RK.AKDLEEE..RT.H.YQG
Retrocopy LKVMTELYQENERKLYRKLIVEENNRLEKE-KLSKVD*MITHAAEELETCRKQAKDLEEEFQRTTHIYQG

Parental  QIISHEKKAHDNWLAARNAERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGP
          .II.HEKKAHDN.LAA..AERNL.DLRKENAHNRQKL.ETE....LLEKDPYALDVPNTAFGREHS.YGP
Retrocopy KIIYHEKKAHDNCLAAWTAERNLDDLRKENAHNRQKLAETEFTIKLLEKDPYALDVPNTAFGREHSSYGP

Parental  SPLGWPSSETRAFLSPPTLLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSD
          SPLG.PSSE.RAFL..PTLLEGPLRLSPLLPGGGGRG.RGPGNPLDHQIT.ERGESSCDR.T.PHRAP.D
Retrocopy SPLGRPSSEMRAFLYLPTLLEGPLRLSPLLPGGGGRGPRGPGNPLDHQITKERGESSCDRFTNPHRAPFD

Parental  TGSLSPPWDQDRRMMFPPPGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMES
          TG.LSPPW.QDRRMM.PPPGQSYPDSALPPQRQDRF.SN..R.SGPAELRSFN.P.LDKMDGSMPSEMES
Retrocopy TGFLSPPWEQDRRMMSPPPGQSYPDSALPPQRQDRFYSNCARRSGPAELRSFNKPPLDKMDGSMPSEMES

Parental  SRNDTKDDLGNLNVPDSSLPAENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGAS
          SRNDTKD.LGNLNVPDSSLPA.NE.TGPGFVPPPLAPIRGPLFPVDTRG.F.RRGPPFPPPPPG.MFGAS
Retrocopy SRNDTKDNLGNLNVPDSSLPAGNEVTGPGFVPPPLAPIRGPLFPVDTRGPFMRRGPPFPPPPPGTMFGAS

Parental  RDYFPPRDFPGPPPAPFAMRNVYPPRGFPPYLPPRPG-FFPPPPHSEGR-SEFPSGLIPPSNEPATEHPE
          .DYFPPRD.PGPP..PFAMRNV.P.RGFPPYLP.RPG.F.PPPPHSE.R.SEFPSGL..PSNEPA.E.PE
Retrocopy PDYFPPRDVPGPPRVPFAMRNVCPLRGFPPYLPLRPG>FPPPPPHSEDR<SEFPSGLSLPSNEPAAEDPE

Parental  PQQET
          PQQET
Retrocopy PQQET

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	0.00 RPM	54.97 RPM
SRP007412_liver	0.00 RPM	36.20 RPM
SRP007412_testis	3.69 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_826 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_826 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_826 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1007

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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,