RetrogeneDB ID: retro_ptro_2345

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:39106583..39107738(+)
• Located in intron of: ENSPTRG00000018126

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFG
• Ensembl ID: ENSPTRG00000015165
• Aliases: None
• Description: None

Sequence

>retro_ptro_2345
ATGAACAGACAGTTGGACCTAAGTGGGAAGGTAATCATGAAAGCTCAACTTGGGGAGGATATTCCAAAAATTCCTATTCA
TAATGAAGATATTAATATTACTTATGATGAATTAGTGCTAATGATGCAACGAGTTTTCAGGGGAAAACTTCTGCGTAATG
TTGAAGTAACAATAAAGTATAAAGATGCAGATGACGATCTTATAACAATTTTTGATAGTTCTGATCTTTCCTTTGCAATT
CAGTGTAGTAGGACACTGAAATTGACATTATTTGTTAATGGCCAACCAAGACCCCTTGAATCAAGTCAGGTGAAATATCT
CTGTCGAGAACTGACAGAACTTTGAAATAAAGTGAATCACTTATTGGATAGCTTGGAACCACCTGGAAAACCAGGACCTT
CCACCAATATTCCTGAAAATGTTACTGTGAATGGTAGGGAAGAAAAGCCTGCTTCTTCGGATTCTTCTGGAAAACAGTCT
ATTCAGGTTATGGCAGCAAGTACGTCAGCTTTTGACCCTTTTAAAAAACCAAGATGAAATAAAAAATAATGTTACGTCGG
CATTTGGCTTAACAGATGATCAGGTTTCAGGGCAACCCAGTGCTCCTGCAGAACACTGTTCAGGAACATCTGACAGCATT
GCCGCCTCCTCCTCAGTAGCAGGTCACCCACCAGGAGTTCAGCCACAGCAACCACCATATACAGAAGCTAAGATACAAGC
AGGTCACACTGAAAGTCAGCTGTATCAATAGTACCAGCAACAGGCTAGCTATGGTGCACAGTGTCTGTGGGCTCTACCTC
AGCAGCCTCAACAGTATGGTATTCAGTATTCAAAAAGCCAGAGTCAGCAGACTGGACTCCAAACAACCTCAGCAGTTCCA
AGGATATGGCCAGCAACCAACTACCCAGGCACCAGCTCCTGCCTTTTTGGTCAGCCTCAACAACTGCCTGCTCAGCTGCC
ACACGGTACCAGGCAAGCAATTATCCTGCACAAATTTATACTACCCAAACTTTTCAGCCTACTAATTATACTGTGGCCCC
TGCCTCTCAACCTAGAATGGCTCCAAGCCAACCTGGGGCCTATAGACCAAGATCAAGTTTTACTTCACTTCCTGTAAGCA
GCATGACCCCTCCTCCAACTGGGCCTAATCCTTAT

Alignment

ORF - retro_ptro_2345 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.52 %
• Parental protein coverage: 95.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MNGQLDLSGKLIIKAQLGEDIRRIPIHNEDI--TYDELVLMMQRVFRGKLLSNDEVTIKYKDEDGDLITI
          MN.QLDLSGK.I.KAQLGEDI..IPIHNEDI..TYDELVLMMQRVFRGKLL.N.EVTIKYKD.D.DLITI
Retrocopy MNRQLDLSGKVIMKAQLGEDIPKIPIHNEDINITYDELVLMMQRVFRGKLLRNVEVTIKYKDADDDLITI

Parental  FDSSDLSFAIQCSRILKLTLFVNGQPRPLESSQVKYLRRELIELRNKVNRLLDSLEPPGEPGPSTNIPEN
          FDSSDLSFAIQCSR.LKLTLFVNGQPRPLESSQVKYL.REL.EL.NKVN.LLDSLEPPG.PGPSTNIPEN
Retrocopy FDSSDLSFAIQCSRTLKLTLFVNGQPRPLESSQVKYLCRELTEL*NKVNHLLDSLEPPGKPGPSTNIPEN

Parental  DTVDGREEKSA-SDSSGKQSTQVMAASMSAFDP-LKNQDEINKNVMSAFGLTDDQVSGPPSAPAEDRSGT
          .TV.GREEK.A.SDSSGKQS.QVMAAS.SAFDP.LKNQDEI..NV.SAFGLTDDQVSG.PSAPAE..SGT
Retrocopy VTVNGREEKPASSDSSGKQSIQVMAASTSAFDP>LKNQDEIKNNVTSAFGLTDDQVSGQPSAPAEHCSGT

Parental  PDSIASSSS-AAHPPGVQPQQPPYTGAQTQAGQIEGQMYQQYQQQAGYGAQQPQAPPQQPQQYGIQYSAS
          .DSIA.SSS.A.HPPGVQPQQPPYT.A..QAG..E.Q.YQ.YQQQA.YGAQ...A.PQQPQQYGIQYS.S
Retrocopy SDSIAASSSVAGHPPGVQPQQPPYTEAKIQAGHTESQLYQ*YQQQASYGAQCLWALPQQPQQYGIQYSKS

Parental  YSQQTGPQ-QPQQFQGYGQQPTSQAPAPAF-SGQPQQLPAQPPQ-QYQASNYPAQTYTAQTSQPTNYTVA
          .SQQTG.Q.QPQQFQGYGQQPT.QAPAPAF..GQPQQLPAQ.P...YQASNYPAQ.YT.QT.QPTNYTVA
Retrocopy QSQQTGLQ>QPQQFQGYGQQPTTQAPAPAF<FGQPQQLPAQLPH<RYQASNYPAQIYTTQTFQPTNYTVA

Parental  PASQPGMAPSQPGAYQPRPGFTSLPGSTMTPPPSGPNPY
          PASQP.MAPSQPGAY.PR..FTSLP.S.MTPPP.GPNPY
Retrocopy PASQPRMAPSQPGAYRPRSSFTSLPVSSMTPPPTGPNPY

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	0.04 RPM	39.54 RPM
SRP007412_cerebellum	0.00 RPM	34.24 RPM
SRP007412_heart	0.00 RPM	19.79 RPM
SRP007412_kidney	0.00 RPM	41.53 RPM
SRP007412_liver	0.03 RPM	59.64 RPM
SRP007412_testis	0.00 RPM	27.40 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2345 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2345 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2345 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3459
Pongo abelii	retro_pabe_2860
Macaca mulatta	retro_mmul_1760

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013928	1 retrocopy	retro_chof_406,
Homo sapiens	ENSG00000114354	1 retrocopy	retro_hsap_3459,
Macaca mulatta	ENSMMUG00000002863	1 retrocopy	retro_mmul_1760,
Nomascus leucogenys	ENSNLEG00000002849	1 retrocopy	retro_nleu_2712,
Ochotona princeps	ENSOPRG00000000781	3 retrocopies	retro_opri_34, retro_opri_849, retro_opri_958,
Pongo abelii	ENSPPYG00000013597	1 retrocopy	retro_pabe_2860,
Pan troglodytes	ENSPTRG00000015165	1 retrocopy	retro_ptro_2345 ,
Pteropus vampyrus	ENSPVAG00000017331	1 retrocopy	retro_pvam_1122,
Ictidomys tridecemlineatus	ENSSTOG00000025779	1 retrocopy	retro_itri_457,