RetrogeneDB ID: retro_ptro_2728

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 8:14192308..14193257(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCDC98
• Ensembl ID: ENSPTRG00000023645
• Aliases: CCDC98, FAM175A
• Description: None

Sequence

>retro_ptro_2728
AGCATTACTGATTGCCAAATAGATGATGCTGAAGTTGTTTATACAATTGACATTCAGAAATATATTCCATGCTATCAGTT
TTTTAGTTTTTATAATTCTTCAGGTGAAGTAAATGAGCAAGCACTGAAGAAAATATTATCAAATTCACAAAGAATGTGGT
AGGTTGGTACAAATTCCATCGTCATTCAGATCACATCATGACATTTAGAGAGAGGCTGCTTCACAAAAACTTGCAGGAGC
ATTTTTCAAACCAAGACCTGGTTTTTCTGCTATGAACACCAAGTATAATAACAGAAAGCCGCTCTACTCATTGACTGGAA
CATGCCTTATATAAACCTCGAAAAGGACTTTTTCACAGGGTACCTTCAGTGGTTGCAAATCTGGGCATGTCTGAACAACT
AGGTTATAAAACTGTATCAGGTTCCTGTATGTCCACTGGTTTTAGCCGAGCAGTACAAACACACAGCTCTAAATTTTTTG
AAGAAGATGGATCCTTAAAGGAGGTACATAAGATAAATGAAATGTATGCTTCATTGTAAGAGGAATTAAAGAGTATATGC
AAAAAAGTGGAAGACAGTGAACAAGCAGTAGATAAACTAGTAAAGGATGTAAACAGATTAAAACGAGAAATTGAAAAAAG
GAGATGAGCCCAGATTCCGGCAGCACGAGAGAAGAGCATCCAAAAAAGACCCTCAGGAGAACATTTTTCTTTGTCAAGCA
TTATGGACCTTTTTTCCAGATTCTGAATTTCTTCATGCATGTGTTATGTCTTTAAAAAAACAGACATGTTTCTAAAGGTA
GCTCTAACAACCACCACCATCTCGATGTAGTAGACAATCTGACCTTAATGGTAGAAAACACTGACATTGCTGAAGCTAGT
CCAGCTAGTACACCACAAATGGTTAAGCATAAAACCTTAGACTTAGCTGACAGATGGCAATTCAAGAGA

Alignment

ORF - retro_ptro_2728 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.34 %
• Parental protein coverage: 77.26 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SITDSQMDDVEVVYTIDIQKYIPCYQLFSFYNSSGEVNEQALKKILSNVK-KNVVGWYKFRRHSDQIMTF
          SITD.Q.DD.EVVYTIDIQKYIPCYQ.FSFYNSSGEVNEQALKKILSN...KNVVGWYKF.RHSD.IMTF
Retrocopy SITDCQIDDAEVVYTIDIQKYIPCYQFFSFYNSSGEVNEQALKKILSNSQ<KNVVGWYKFHRHSDHIMTF

Parental  RERLLHKNLQEHFSNQDLVFLLLTPSIITESCSTHRLEHSLYKPQKGLFHRVPLVVANLGMSEQLGYKTV
          RERLLHKNLQEHFSNQDLVFLL.TPSIITES.STH.LEH.LYKP.KGLFHRVP.VVANLGMSEQLGYKTV
Retrocopy RERLLHKNLQEHFSNQDLVFLL*TPSIITESRSTH*LEHALYKPRKGLFHRVPSVVANLGMSEQLGYKTV

Parental  SGSCMSTGFSRAVQTHSSKFFEEDGSLKEVHKINEMYASLQEELKSICKKVEDSEQAVDKLVKDVNRLKR
          SGSCMSTGFSRAVQTHSSKFFEEDGSLKEVHKINEMYASL.EELKSICKKVEDSEQAVDKLVKDVNRLKR
Retrocopy SGSCMSTGFSRAVQTHSSKFFEEDGSLKEVHKINEMYASL*EELKSICKKVEDSEQAVDKLVKDVNRLKR

Parental  EIEKRRGAQIQAAREKNIQ-KDPQENIFLCQALRTFFPNSEFLHSCVMSL-KNRHVSKSSCNYNHHLDVV
          EIEKRR.AQI.AAREK.IQ.KDPQENIFLCQAL.TFFP.SEFLH.CVMSL.KNRHVSK.S.N..HHLDVV
Retrocopy EIEKRR*AQIPAAREKSIQ>KDPQENIFLCQALWTFFPDSEFLHACVMSL>KNRHVSKGSSNNHHHLDVV

Parental  DNLTLMVEHTDIPEASPASTPQIIKHKALDLDDRWQFKR
          DNLTLMVE.TDI.EASPASTPQ..KHK.LDL.DRWQFKR
Retrocopy DNLTLMVENTDIAEASPASTPQMVKHKTLDLADRWQFKR

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	0.05 RPM	1.79 RPM
SRP007412_cerebellum	0.29 RPM	3.05 RPM
SRP007412_heart	0.03 RPM	3.15 RPM
SRP007412_kidney	0.21 RPM	4.55 RPM
SRP007412_liver	0.03 RPM	1.64 RPM
SRP007412_testis	0.11 RPM	26.35 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2728 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2728 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2728 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4024
Pongo abelii	retro_pabe_3301

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013241	1 retrocopy	retro_chof_2580,
Homo sapiens	ENSG00000163322	1 retrocopy	retro_hsap_4024,
Macaca mulatta	ENSMMUG00000015357	2 retrocopies	retro_mmul_1499, retro_mmul_2320,
Nomascus leucogenys	ENSNLEG00000009133	2 retrocopies	retro_nleu_1198, retro_nleu_661,
Pongo abelii	ENSPPYG00000014898	2 retrocopies	retro_pabe_2208, retro_pabe_3301,
Pan troglodytes	ENSPTRG00000023645	2 retrocopies	retro_ptro_1911, retro_ptro_2728 ,