RetrogeneDB ID: retro_ptro_2524

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:47568359..47569697(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDC14B
• Ensembl ID: ENSPTRG00000021155
• Aliases: None
• Description: None

Sequence

>retro_ptro_2524
AAGCGGAAAAGCAAGGGGCGGACGAGCTGGGCCGCCGCGCCCCCATGCTCGCCGCGCTGCTCTTTGACCTCGCCGGGTGT
GAAGAAGATGCGCAGCTCCACGCAGCAGGACCCGCGCCGCCGGGACCCCCAGGACGACGTGTACCTGGACATCACCGATC
GCCTTCGTTTTGCCATTCTCTACAGCAGACCAAAGAGTGCATCAAATGTACATTATTTCAGCATAGATAATGAACTCGAA
TATGAGAACTTCTCCGAAGACTTTGGACCACTCAATCTGGCAATGGTTTACAGATATTGTTGCAAGATAAATAAGAAATT
AAAGTCCATTACAATGTTAAGGAAGAAAATTGTTCATTTTACTGGCTCTGATCAGAGAAAACAAGCAAATGCTGCCTTCC
TTGTTGGATGCTACATGGTTATATACTTGGGGAGAACCCCAGAAGCAGCATATAGAATATTAATCTTTGGAGATACACCC
TATATTCCTTTCAGAGATGCTGCCTACGGAAGCTGCAATTTCTACATTACACTTCTTGACTGTTTTCATGCAGTAAAGAA
GGCAATGCAGTATGGCTTCCTTAATTTCAACTCATTTAACCTTGATGAATACGAACACTATGAAAAAGCAGAAAACGGAG
ATTTAAATTGGATAATACCAGACCGATTTATTGCCTTCTGTGGACCTCATTCAAGAGCCAGACTTGAAAGTGGTTACCAC
CAACATTCTCCCGAGACTTATATTCAATATTTTAAGAATCACAATGTTACTACCATTATTCGTCTGAATAAAAGGATGTA
TGATGCCAAACGCTTTACGGATGCTGGCTTCGATCACCATGATCTTTTCTTTGCGGATGGCAGCACCCCTACTGATGCCA
TTGTCAAAAGATTTCTGGATATCTGTGAAAATGCTGAGGGTGCCATTGCAGTACACTGTAAAGCTGGCCTTGGTCGCACG
GGCACTCTGATAGCCTGCTACATCATGAAGCATTACAGGATGACAGCAGCCGAGACCATTGCGTGGGTAAGGATCTGCAG
ACCTGGCTTGGTGATTGGGCCTCAGCAGCAGTTTTTGGTGATGAAGCAAACAAGCCTCTGGCTGGAAGGGGACTATTTTC
GTCAGAAGTTAAAGGGGCAGGAGAATGGACAACACAGAGCAGCCTTCTCCAAACTTCTCTCTGGTGTTGATGACATTTCC
ATAAATGGGGTCGAGAATCAAGACCAGCAAGAACCCAAACCTTACAGTGATGATGACGAAATCAATGGAGTGACACAAGG
TGATAGACGTCGGGCCCTGAAAAGGCGAAGACAATCAAAAACAAAAGATATTCTTCTC

Alignment

ORF - retro_ptro_2524 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.29 %
• Parental protein coverage: 89.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRKSERRSSWAAAPPCSRRCSSTSPGVKKIRSSTQQDPRRRDPQDDVYLDITDRLCFAILYSRPKSASNV
          KRKS..R.SWAAAPPCS.RCS.TSPGVKK.RSSTQQDPRRRDPQDDVYLDITDRL.FAILYSRPKSASNV
Retrocopy KRKSKGRTSWAAAPPCSPRCSLTSPGVKKMRSSTQQDPRRRDPQDDVYLDITDRLRFAILYSRPKSASNV

Parental  HYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMV
          HYFSIDNELEYENF..DFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMV
Retrocopy HYFSIDNELEYENFSEDFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMV

Parental  IYLGRTPEEAYRILIFGETSYIPFRDAAYGSCNFYITLLDCFHAVKKAMQYGFLNFNSFNLDEYEHYEKA
          IYLGRTPE.AYRILIFG.T.YIPFRDAAYGSCNFYITLLDCFHAVKKAMQYGFLNFNSFNLDEYEHYEKA
Retrocopy IYLGRTPEAAYRILIFGDTPYIPFRDAAYGSCNFYITLLDCFHAVKKAMQYGFLNFNSFNLDEYEHYEKA

Parental  ENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKNHNVTTIIRLNKRMYDAKRFTDAGFDHH
          ENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKNHNVTTIIRLNKRMYDAKRFTDAGFDHH
Retrocopy ENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKNHNVTTIIRLNKRMYDAKRFTDAGFDHH

Parental  DLFFADGSTPTDAIVKEFLDICENAEGAIAVHCKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGS
          DLFFADGSTPTDAIVK.FLDICENAEGAIAVHCKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPG.
Retrocopy DLFFADGSTPTDAIVKRFLDICENAEGAIAVHCKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGL

Parental  VIGPQQQFLVMKQTNLWLEGDYFRQKLKGQENGQHRAAFSKLLSGVDDISINGVENQDQQEPEPYSDDDE
          VIGPQQQFLVMKQT.LWLEGDYFRQKLKGQENGQHRAAFSKLLSGVDDISINGVENQDQQEP.PYSDDDE
Retrocopy VIGPQQQFLVMKQTSLWLEGDYFRQKLKGQENGQHRAAFSKLLSGVDDISINGVENQDQQEPKPYSDDDE

Parental  INGVTQGDRLRALKSRRQSKTNAIPL
          INGVTQGDR.RALK.RRQSKT..I.L
Retrocopy INGVTQGDRRRALKRRRQSKTKDILL

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	0.02 RPM	18.64 RPM
SRP007412_cerebellum	0.00 RPM	6.24 RPM
SRP007412_heart	0.03 RPM	18.39 RPM
SRP007412_kidney	0.05 RPM	35.17 RPM
SRP007412_liver	0.00 RPM	30.64 RPM
SRP007412_testis	10.43 RPM	58.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2524 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2524 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2524 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000081377	2 retrocopies	retro_hsap_3729, retro_hsap_3845,
Macaca mulatta	ENSMMUG00000005997	1 retrocopy	retro_mmul_1615,
Nomascus leucogenys	ENSNLEG00000016822	1 retrocopy	retro_nleu_1981,
Pongo abelii	ENSPPYG00000019417	1 retrocopy	retro_pabe_208,
Pan troglodytes	ENSPTRG00000021155	2 retrocopies	retro_ptro_2524 , retro_ptro_2621,
Ictidomys tridecemlineatus	ENSSTOG00000012205	1 retrocopy	retro_itri_1799,
Ictidomys tridecemlineatus	ENSSTOG00000028527	3 retrocopies	retro_itri_1798, retro_itri_1821, retro_itri_1890,