RetrogeneDB ID: retro_ptro_1899

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 3:74500699..74501472(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC75
• Ensembl ID: ENSPTRG00000011832
• Aliases: None
• Description: Coiled-coil domain containing 75 [Source:UniProtKB/TrEMBL;Acc:K7B703]

Sequence

>retro_ptro_1899
ATGGCAGAAGAAGAGGACTAACATCTGATTCCTTCATTAATGTCCAAGAAGATATCAGACCAGGCTTGCCAATGCTAAGG
CAAATCCGGGAAGCCCGTGGAAAAGAAGAAAAGCAACAGGAAGCTAACTTGAAACACAGGCAGAAGAGTTTAAAAGAAGA
AGAACAAAAAAGACGTAACAATGGGTTGAAGAATGCACTAGGCTGTGAAACAAAGGGTTTGCCTTGCTCCAAAAGATGGG
CTATAAAAGTGGTCAGGCACTTGGCAAGGGTAGGAGTGGTATTGTTGAACCCATTCCTCTCAATATCAAAACAGGGAAAA
GTGGCATTTGGTCATAAGGCATCATTAAAACGGAAAGCAGAGGAAAAATTAGAAAGCTACGGAAAAAAGATTCACATGAA
TAACCAAGCTGAAGAAAAAGCTGCAGACCAGTTTCGAATGCGACTTAAAAATAAGCAAGATGAAATGAAGCTAGAAGGAG
ATCACAGAAGAAGCCAGCGAGTCTGTCAACAATTGGACACCCAGAAAAATATTCAGGTTCCCAGGGAAGCATGGTACTGG
TTGAGGCTTGAAAAGGAGACTGAAGATGAAGAAGAAAAAGAACAGGATGAAGATGAATATAAGAGTGAAGATTTAAGTGT
ACTGGAAAAATTACAAATATTGACTAGTTATTTAAGAGAAGAACTTCTGTATAGTATTTGGTGTGGAACAGCCTATGAAG
ATAAAGAAGACCTATCTTCAAATTGTCCAGGACCAACTTCTGCAGATCATGAC

Alignment

ORF - retro_ptro_1899 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.69 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAEEED-YMSDSFINVQEDIRPGLPMLRQIREARRKEEKQQEANLKNRQKTLKEEEQERRDIGLKNALGC
          MAEEED...SDSFINVQEDIRPGLPMLRQIREAR.KEEKQQEANLK.RQK.LKEEEQ.RR..GLKNALGC
Retrocopy MAEEED<LTSDSFINVQEDIRPGLPMLRQIREARGKEEKQQEANLKHRQKSLKEEEQKRRNNGLKNALGC

Parental  E-NKGFALLQKMGYKSGQALGKSGGGIVEPIPLNIKTGKSGI-GHEASLKRKAEEKLESYRKKIHMKNQA
          E.NKGFALLQKMGYKSGQALGK...GIVEPIPLNIKTGKSGI.GH.ASLKRKAEEKLESY.KKIHM.NQA
Retrocopy E<NKGFALLQKMGYKSGQALGKGRSGIVEPIPLNIKTGKSGI>GHKASLKRKAEEKLESYGKKIHMNNQA

Parental  EEKAAEQFRMRLKNKQDEVKLEGDLRRSQRACQQLDVQKNIQVPREAWYWLRLEEETEEDEEEKEQDEDE
          EEKAA.QFRMRLKNKQDE.KLEGD.RRSQR.CQQLD.QKNIQVPREAWYWLRLE.ET.EDEEEKEQDEDE
Retrocopy EEKAADQFRMRLKNKQDEMKLEGDHRRSQRVCQQLDTQKNIQVPREAWYWLRLEKET-EDEEEKEQDEDE

Parental  YKSEDLSVLEKLQILTSYLREEHLYCIWCGTAYEDKEDLSSNCPGPTSAAHD
          YKSEDLSVLEKLQILTSYLREE.LY.IWCGTAYEDKEDLSSNCPGPTSA.HD
Retrocopy YKSEDLSVLEKLQILTSYLREELLYSIWCGTAYEDKEDLSSNCPGPTSADHD

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	3.79 RPM
SRP007412_cerebellum	0.00 RPM	9.36 RPM
SRP007412_heart	0.00 RPM	3.18 RPM
SRP007412_kidney	0.00 RPM	2.56 RPM
SRP007412_liver	0.00 RPM	1.31 RPM
SRP007412_testis	0.32 RPM	51.43 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1899 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1899 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1899 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2802

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006041	1 retrocopy	retro_cfam_708,
Choloepus hoffmanni	ENSCHOG00000004377	3 retrocopies	retro_chof_1420, retro_chof_2292, retro_chof_398,
Homo sapiens	ENSG00000152133	1 retrocopy	retro_hsap_2802,
Monodelphis domestica	ENSMODG00000015289	1 retrocopy	retro_mdom_1855,
Nomascus leucogenys	ENSNLEG00000027017	1 retrocopy	retro_nleu_1542,
Pan troglodytes	ENSPTRG00000011832	1 retrocopy	retro_ptro_1899 ,