RetrogeneDB ID: retro_ptro_868

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:51645526..51647568(-)
• 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_868
ACAGAAGCACAAAGTCTGGAGGCAAACTGTGAAAAGCTGAACAGGTCCAATTCTGAACTGGAGCATGAAATACTCTGTCT
AGAAAAGGGGTTAAAAGAAGAGAAATCTAAACATTCTGAACAAGATGAGGTGATGGCGGATATTTCCAAAAAGATACAGT
CTCTAGAAGATGAGTCAAAATCCCTCAAATCACTACTAGCTGAAGCCAAAATGACCTTCAAGAGATTTCAAATGAATGAA
GAAAAACTGGAGATAGCAATACAAGATGCTTCGAGTGAAAATTGTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGA
AGCTGAAGTATGGAAAGAACAAGTGAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTACATGCAGAAC
AAGTTCTAAATGATAAAGAAAATCACATCGAGACTCTGACTGAACGCTTGCTAAAGATCAAAGATCGGGCTGCTATGCTG
GAAGAAGACATAACGGATGATGGTAACTTGGAATTAGAAATGAACAGTGAATCGGAAGATGGTGCTTACTTAGATAATCC
TCCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGAAAGAAACC
AAATTTATATACGGTTATCTAAAGTTGATAAAACCAAGGAAGAGCTTAGAGGGCATATTAAAAATCTTCAGACGGAACAA
GCATCTTTGCAGTCGGAAAACACACATTTTGAAAGTGAGAATCAGAAACTTCAACAGAAAGTTAAAGTAATGACTGAGTT
ATGTCAAGAAAATGAAATGAAACTCTACAGGAAATTAATAGTAGAGGAAAATAACCGGTTAGAGAAAGAGAAACTTTCTA
AAGTAGACGAAATGATCAGCCATGCCACTGAAGAGCTGGAGACCTGCAGAAAGCGAGCCAAAGATCTTGAAGAAGAAACT
TGAGAGAACTATTCATTTTTATCAAGGGAAGATTATATACCATGAGAAAAAAGCACATGATAATTGTTTGGCAGCATGGA
CTGCTGAAAGAAACCTCAATGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAGCTGAAACAGAGTTTAAAATT
AAACTTTTAGAAAAAGATCCTTATGCACTTGATGTTCCAAATACAGCATTTGGCAGAGAGCATTCCTCATATGGTCCCTC
ACCATTGGGTCGGCCTTCATCTGAAACGAGAGCTTTTCTCTATCCTCCAACTTTGTTGGAGGGTCCACTCAGACTCTCAC
CTTTGCTTCCAGCGGGAGGAGGAAGAGGCTTAAGAGGCCCAGGGAATCCTCTGGACCACCAGATTACCAATGAAAGAGGA
GAATCAAGCTGTGATAGGTTAACCGATCCTCACAAGGCTCCTTCTGACACTGGGCCCCTGTCACCTCCGTGGGAACAGGA
CCGTAGGATGATGTTTCCTCCACCAGGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGATTTTATT
CTAATTGTGCTAGACGCTCTGGACCAGCAGAACTCAGAAGTTTTAATATACCTTCTTTGGATAAAATGGATGGGTCAATG
CCTTCAGAAATGGAATCCAGTGGAAATGATACCAAAGATAAACTTGGTAATCTAAATGTGCCTGATTCATCTCTCCCCGC
TGAAACTGAAGCAACTGGCCCTGGCTTTGTTCCTCCACCTCTTGCTTCAATCAGAGGTCCGTTGTTTCCAGTGGATACGA
GGGGCCCGTTCATGAGGAGAGGACCTCCTTTCCCTCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTT
CCACCAAGGGATGTCCCAGGTCCACGTGCTCCATTTGCAATGAGAAATGTCTGTCCACCGAGGGGTTTTCCTCCTTACCT
TCCCCCAAGACCTGGATTTCCCCCCTACCCGCACATTCTGAAGGTAGAGTGAGTTCCCTTCAGGGTTGAGTCTGCCTTCA
AATGAGCCTGCTGCTGAAGATCCAGAACCACGGCAAGAAACC

Alignment

ORF - retro_ptro_868 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 84.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSERDELMADISKRIQSLEDESKSLKSQVAEAK
          TEAQSLEA.CEKLNRSNSELE.EILCLEK.LKEEKSKHSE.DE.MADISK.IQSLEDESKSLKS..AEAK
Retrocopy TEAQSLEANCEKLNRSNSELEHEILCLEKGLKEEKSKHSEQDEVMADISKKIQSLEDESKSLKSLLAEAK

Parental  MTFKIFQMNEERLKIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVTFEDSEVHAEQVLNDKE
          MTFK.FQMNEE.L.IAI.DA..EN.QLQESQKQLLQEAEVWKEQVSELNKQK.TFEDS.VHAEQVLNDKE
Retrocopy MTFKRFQMNEEKLEIAIQDASSENCQLQESQKQLLQEAEVWKEQVSELNKQKITFEDSKVHAEQVLNDKE

Parental  SHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLEG
          .HI.TLTERLLK.KD.AAML.EDITDD.NLELEMNSESE.GAYLDNPPKGALKKLIHAAKLNASL.TLEG
Retrocopy NHIETLTERLLKIKDRAAMLEEDITDDGNLELEMNSESEDGAYLDNPPKGALKKLIHAAKLNASLTTLEG

Parental  ERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKLT
          ERNQIYI.LS.VDKTKEEL..HIKNLQTEQASLQSENTHFE.ENQKLQQK.KVMTEL.QENEMKL.RKL.
Retrocopy ERNQIYIRLSKVDKTKEELRGHIKNLQTEQASLQSENTHFESENQKLQQKVKVMTELCQENEMKLYRKLI

Parental  VEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEE-LERTIHSYQGQIISHEKKAHDNWLAARNA
          VEEN.RLEKE.KLSKVDE.ISHATEELET.RKRAKDLEEE.LERTIH.YQG.II.HEKKAHDN.LAA..A
Retrocopy VEENNRLEKE-KLSKVDEMISHATEELETCRKRAKDLEEE>LERTIHFYQGKIIYHEKKAHDNCLAAWTA

Parental  ERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPTL
          ERNLNDLRKENAHNRQKL.ETE.K..LLEKDPYALDVPNTAFGREHS.YGPSPLG.PSSETRAFL.PPTL
Retrocopy ERNLNDLRKENAHNRQKLAETEFKIKLLEKDPYALDVPNTAFGREHSSYGPSPLGRPSSETRAFLYPPTL

Parental  LEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPPP
          LEGPLRLSPLLP.GGGRG.RGPGNPLDHQITNERGESSCDRLTDPH.APSDTG.LSPPW.QDRRMMFPPP
Retrocopy LEGPLRLSPLLPAGGGRGLRGPGNPLDHQITNERGESSCDRLTDPHKAPSDTGPLSPPWEQDRRMMFPPP

Parental  GQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSSL
          GQSYPDSALPPQRQDRF.SN..R.SGPAELRSFN.PSLDKMDGSMPSEMESS.NDTKD.LGNLNVPDSSL
Retrocopy GQSYPDSALPPQRQDRFYSNCARRSGPAELRSFNIPSLDKMDGSMPSEMESSGNDTKDKLGNLNVPDSSL

Parental  PAENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPPAPFAM
          PAE.EATGPGFVPPPLA.IRGPLFPVDTRG.F.RRGPPFPPPPPG.MFGAS.DYFPPRD.PG.P.APFAM
Retrocopy PAETEATGPGFVPPPLASIRGPLFPVDTRGPFMRRGPPFPPPPPGTMFGASPDYFPPRDVPG-PRAPFAM

Parental  RNVYPPRGFPPYLPPRPGF-FPPPPHSEGR-SEFPSGLIPPSNEPATEHPEPQQET
          RNV.PPRGFPPYLPPRPGF..P.P.HSEGR.SEFPSGL..PSNEPA.E.PEP.QET
Retrocopy RNVCPPRGFPPYLPPRPGF<SPLPAHSEGR<SEFPSGLSLPSNEPAAEDPEPRQET

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	0.21 RPM	10.90 RPM
SRP007412_cerebellum	0.29 RPM	9.86 RPM
SRP007412_heart	0.06 RPM	11.02 RPM
SRP007412_kidney	0.05 RPM	54.97 RPM
SRP007412_liver	0.00 RPM	36.20 RPM
SRP007412_testis	6.22 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_868 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_868 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1055

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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,