RetrogeneDB ID: retro_ptro_821

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 13:49611134..49613075(+)
• 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_821
ACAGAAGCACAAAGTCTGGAGGCAAACTGTGAAAAGCTGAACAGGTCCAATTCTGAACTGGAGCATGAAATACTCTGTCT
AGAAAAGGGGTTAAAAGAAGAGAAATCTAAACATTCTGAACAAGATGAGGTGATGGCGGATATTTCCAAAAGGATACAGT
CTCTAGAAGATGAGTCAAAATCCCTAAAATCACTACTAGCTGAAGCCAAAATGACCTTCAAGAGATTTCAAATGAATTAA
GAACAAAGAAGATAGCAATACAAGATGCTTTGAATGAAAATTGTCAACTTCAGGAAAGCCAGAAACAGCTTTTGCAAGAA
GCTGAAGTATGGAAAGAACAAGTGAGTGAACTTAATAAACAGAAAATAACATTTGAAGACTCCAAAGTACACGCAGAACA
AGTTCTAAATGATAAAGAAAATCACATCGAGACTCTGACTGAACGCTTGCTAAAGATCAAAGATCGGGCTGCTATGCTGG
AAGAAGACATAACGGATGATGAAAACTTGGAATTAGAAATGAACAGTGAATCGGAAGATGGCGCTTACTTAGATAATCCT
CCAAAAGGAGCTTTGAAGAAACTGATTCATGCTGCTAAGTTAAATGCTTCTTTAACAACCTTAGAAGGAGAAAGAAACCA
AATTTATATACGGTTATCTAAAGTTGATAAAACCAAGGAAGAGCTTAGAGGGCATATTAAAAATCTTTAGATGGAACAAG
CATCTTTGCAGTCAGAAAACACATATTTTGAAAGTGAGAATCAGAAGCTTCAACAGAAACTTAAGGTAATGACTGAATTA
TATCAAGAAAATGAAATGAAACTCTACAGGAAATTAATAGTAGAGGAAAATAACCGGCTAGAGAAAGAGAAATTTTCTAA
AGTAGACGAAATGATCAGCCATGCCACTGAGGAGCTGGAGACCTACAGAAAGCGAGCCAAATATCTTGAAGAAGAAACTT
GAGAGAACTATTCATTTTTATCAAGGGAAGATTATATACCATGAGAAAAAAGCACATGATAATTGTTTGACAGCACAGAC
TGCTGAAAGTAACCTCAATGATTTAAGGAAAGAAAATGCTCACAACAGACAAAAATTAATTGAAACAGACTTTAAAATTA
AATTTTTAGAAAAAGATCCTTATGCACTTGATGTTCCAAATACAGCATTTGGCAGAGAGCATTCCTCATATGGTCCCTCA
CCATTGCGTTGGCCTTCATCTGAAACGAGAGCTTTTCTCTATCCTCCAACTTTGTCGGAGGGTCCACTCAGACTCTCACC
TTTCCCTCCAGGGGGAGGAGGAAGAGGCCCAAGAGGCCCAGGGAATCCTCTGGACCACCAGATTACCAGTGAAAGAGGAT
AATCAAGCTGTGATAGGTTTACTGATCCTCACAAGGCTCCTTCTGACACTGGGCCCCTGTCACCTCCGTGGGAACAGGAC
CGTAGGATGATGTTTCCTCCACCAGGACAATCATATCCTGATTCAGCTCTTCCTCCACAAAGGCAAGACAGGTTTTATTC
TAATTCTGCTAGACGCTCTGGACCAGCAGAACTCAGAAGTTTTAATATGCCTTCTTTGGATAAAATGGATAGGTCAGTGC
ATTCAGAAATGGAATTCAGTGGAAATTATACCAAAGATAATCTTGGTAATTTAAATGTGCCTGATTCATCTCTCCCCGCT
GAAACTGAAGCAACTGGCCCTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCAGTGGATACGAG
GGGCCCGTTCATGAGGAGAGGACCTCCTTTCCCTCCACCTCCTCCAGGAACCATGTTTGGAGCTTCTCCAGATTATTTTC
CACCAAGGGATGTCCCAGGTCCACCACGTGCTCCATTTGCAATGAGAAATGTCTGTCCACCGAGGGGTTTTCCTCCTTAC
CTTCCCCCAAGACCTGGATTT

Alignment

ORF - retro_ptro_821 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.92 %
• Parental protein coverage: 80.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TEAQSLEATCEKLNRSNSELEDEILCLEKELKEEKSKHSERDELMADISKRIQSLEDESKSLKSQVAEAK
          TEAQSLEA.CEKLNRSNSELE.EILCLEK.LKEEKSKHSE.DE.MADISKRIQSLEDESKSLKS..AEAK
Retrocopy TEAQSLEANCEKLNRSNSELEHEILCLEKGLKEEKSKHSEQDEVMADISKRIQSLEDESKSLKSLLAEAK

Parental  MTFKIFQMNEERL-KIAIKDALNENSQLQESQKQLLQEAEVWKEQVSELNKQKVTFEDSEVHAEQVLNDK
          MTFK.FQMN.E...KIAI.DALNEN.QLQESQKQLLQEAEVWKEQVSELNKQK.TFEDS.VHAEQVLNDK
Retrocopy MTFKRFQMN*EQR<KIAIQDALNENCQLQESQKQLLQEAEVWKEQVSELNKQKITFEDSKVHAEQVLNDK

Parental  ESHIKTLTERLLKMKDWAAMLGEDITDDDNLELEMNSESENGAYLDNPPKGALKKLIHAAKLNASLKTLE
          E.HI.TLTERLLK.KD.AAML.EDITDD.NLELEMNSESE.GAYLDNPPKGALKKLIHAAKLNASL.TLE
Retrocopy ENHIETLTERLLKIKDRAAMLEEDITDDENLELEMNSESEDGAYLDNPPKGALKKLIHAAKLNASLTTLE

Parental  GERNQIYIQLSEVDKTKEELTEHIKNLQTEQASLQSENTHFENENQKLQQKLKVMTELYQENEMKLHRKL
          GERNQIYI.LS.VDKTKEEL..HIKNL..EQASLQSENT.FE.ENQKLQQKLKVMTELYQENEMKL.RKL
Retrocopy GERNQIYIRLSKVDKTKEELRGHIKNL*MEQASLQSENTYFESENQKLQQKLKVMTELYQENEMKLYRKL

Parental  TVEENYRLEKEEKLSKVDEKISHATEELETYRKRAKDLEEE-LERTIHSYQGQIISHEKKAHDNWLAARN
          .VEEN.RLEKE.K.SKVDE.ISHATEELETYRKRAK.LEEE.LERTIH.YQG.II.HEKKAHDN.L.A..
Retrocopy IVEENNRLEKE-KFSKVDEMISHATEELETYRKRAKYLEEE>LERTIHFYQGKIIYHEKKAHDNCLTAQT

Parental  AERNLNDLRKENAHNRQKLTETELKFELLEKDPYALDVPNTAFGREHSPYGPSPLGWPSSETRAFLSPPT
          AE.NLNDLRKENAHNRQKL.ET..K...LEKDPYALDVPNTAFGREHS.YGPSPL.WPSSETRAFL.PPT
Retrocopy AESNLNDLRKENAHNRQKLIETDFKIKFLEKDPYALDVPNTAFGREHSSYGPSPLRWPSSETRAFLYPPT

Parental  LLEGPLRLSPLLPGGGGRGSRGPGNPLDHQITNERGESSCDRLTDPHRAPSDTGSLSPPWDQDRRMMFPP
          L.EGPLRLSP..PGGGGRG.RGPGNPLDHQIT.ERG.SSCDR.TDPH.APSDTG.LSPPW.QDRRMMFPP
Retrocopy LSEGPLRLSPFPPGGGGRGPRGPGNPLDHQITSERG*SSCDRFTDPHKAPSDTGPLSPPWEQDRRMMFPP

Parental  PGQSYPDSALPPQRQDRFCSNSGRLSGPAELRSFNMPSLDKMDGSMPSEMESSRNDTKDDLGNLNVPDSS
          PGQSYPDSALPPQRQDRF.SNS.R.SGPAELRSFNMPSLDKMD.S..SEME.S.N.TKD.LGNLNVPDSS
Retrocopy PGQSYPDSALPPQRQDRFYSNSARRSGPAELRSFNMPSLDKMDRSVHSEMEFSGNYTKDNLGNLNVPDSS

Parental  LPAENEATGPGFVPPPLAPIRGPLFPVDTRGAFLRRGPPFPPPPPGAMFGASRDYFPPRDFPGPPPAPFA
          LPAE.EATGPGFVPPPLAPIRGPLFPVDTRG.F.RRGPPFPPPPPG.MFGAS.DYFPPRD.PGPP.APFA
Retrocopy LPAETEATGPGFVPPPLAPIRGPLFPVDTRGPFMRRGPPFPPPPPGTMFGASPDYFPPRDVPGPPRAPFA

Parental  MRNVYPPRGFPPYLPPRPGF
          MRNV.PPRGFPPYLPPRPGF
Retrocopy MRNVCPPRGFPPYLPPRPGF

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	0.03 RPM	54.97 RPM
SRP007412_liver	0.00 RPM	36.20 RPM
SRP007412_testis	6.53 RPM	20.44 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_821 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_821 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_821 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1201

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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,