RetrogeneDB ID: retro_pabe_208

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:35041106..35042483(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000017566
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CDC14B
• Ensembl ID: ENSPPYG00000019417
• Aliases: None
• Description: cell division cycle 14B [Source:HGNC Symbol;Acc:1719]

Sequence

>retro_pabe_208
ATGAAGCGGAAAAGCGAGGGGCGGTCGAGCTGGGCCGCCGCGCCCCGCTGCTCGCCGCGCTGCTCTTTGACCTCGCTGGG
CGTGAAGAAGATCCGCAGCTCCACGCAGCAGGACTCGCGCCTCCGGGACCCCCAGGACGACGTGTACCTGGACATCACCG
ATCGCCTTCGTTTTGCCATTCTCTACAGCAGACCAAAGAGTGCATCAAATGTACATTATTTCAGCATAGATAATGAACTC
GAATATGAGAACTTCTCCGAAGACTTTGGACCACTCAATCTGGCAATGGTTTACAGATATTGTTGCAAGATAAATAAGAA
ATTAAAGTCCATTACAATGTTAAGGAAGAAAATTGTTCATTTTACTGGCTCTGATCAGAGAAAACAAGCAAATGCTGCCT
TCCTTGTTGGATGCTACATGGTTATATATTTGGGGAGAACCCCAGAAGAAGCATATAGAATATTAATCTTTGGAGATACA
TCCTATATTCCTTTCAGAGATGCTGCCTATGGAAGCTGCAATTTCTACATTACACTTCTTGACTGTTTTCATGCAGTAAA
GAAGGCAATGCAGTATGGCTTCCTTAATTTCAACTCATTTAACCTTGATGAATATGAACACTATGAAAAAGCAGAAAACG
GAGATTTAAATTGGATAATACCAGACCGATTTATTGCCTTCTGTGGACCTCATTCAAGAGCCAGACTTGAAAGTGGTTAC
CACCAACATTCTCCCGAGACTTATATTCAATATTTTAAGAATCACAATGTTACTACCATTATTCGTCTGAATAAAAGGAT
GTATGATGCCAAACGCTTTACGGATGCTGGCTTCGATCACCATGATCTTTTCTTTGCGGATGGCAGCACCCCTACTGATG
CCATAGTCAAAGGATTTCTGGATATCTGTGAAAATGCTGAGGGTGCCATTGCAGTACATTGTAAAGCTGGCCTTGGTCGC
ACGGGCACTCTGATAGCCTGCTACATCATGAAGCATTACAGGATGACAGCAGCCGAGACCATTGCGTGGGTAAGGATCTG
CAGACCTGGCTTGGTGATTGGGCCTCAGCAGCAGTTTTTGGTGATGAAGCAAACAAGCCTCTGGCTGGAAGGGGACTATT
TTCGTCGGAAGTTAAAGGGGCAGGAGAATGGACAACACAGAGCAGCCTTCTCCAAACTTCTCTCTGGTGTTGATGACATT
TCCATAAATGGGGTCGAGAATCAAGACCAGCAAGAACCTGAACCTTACAGTGATGACGACGAAATCAATGGAGTGACACA
AGGTGATAGACTTCGGGCCCTGAAAAGCCAAAGACAGTCAAAAACAAACGCTATTCTTCTCACATGTCCCCTGGCTGTGC
TGACCTCTGCACTGTGT

Alignment

ORF - retro_pabe_208 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.21 %
• Parental protein coverage: 89.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKRKSERRSSWAAAPPCSRRCSSTSPGVKKIRSSTQQDPRRRDPQDDVYLDITDRLCFAILYSRPKSASN
          MKRKSE.RSSWAAAP.CS.RCS.TS.GVKKIRSSTQQD.R.RDPQDDVYLDITDRL.FAILYSRPKSASN
Retrocopy MKRKSEGRSSWAAAPRCSPRCSLTSLGVKKIRSSTQQDSRLRDPQDDVYLDITDRLRFAILYSRPKSASN

Parental  VHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYM
          VHYFSIDNELEYENF..DFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYM
Retrocopy VHYFSIDNELEYENFSEDFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYM

Parental  VIYLGRTPEEAYRILIFGETSYIPFRDAAYGSCNFYITLLDCFHAVKKAMQYGFLNFNSFNLDEYEHYEK
          VIYLGRTPEEAYRILIFG.TSYIPFRDAAYGSCNFYITLLDCFHAVKKAMQYGFLNFNSFNLDEYEHYEK
Retrocopy VIYLGRTPEEAYRILIFGDTSYIPFRDAAYGSCNFYITLLDCFHAVKKAMQYGFLNFNSFNLDEYEHYEK

Parental  AENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKNHNVTTIIRLNKRMYDAKRFTDAGFDH
          AENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKNHNVTTIIRLNKRMYDAKRFTDAGFDH
Retrocopy AENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKNHNVTTIIRLNKRMYDAKRFTDAGFDH

Parental  HDLFFADGSTPTDAIVKEFLDICENAEGAIAVHCKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPG
          HDLFFADGSTPTDAIVK.FLDICENAEGAIAVHCKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPG
Retrocopy HDLFFADGSTPTDAIVKGFLDICENAEGAIAVHCKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPG

Parental  SVIGPQQQFLVMKQTNLWLEGDYFRQKLKGQENGQHRAAFSKLLSGVDDISINGVENQDQQEPEPYSDDD
          .VIGPQQQFLVMKQT.LWLEGDYFR.KLKGQENGQHRAAFSKLLSGVDDISINGVENQDQQEPEPYSDDD
Retrocopy LVIGPQQQFLVMKQTSLWLEGDYFRRKLKGQENGQHRAAFSKLLSGVDDISINGVENQDQQEPEPYSDDD

Parental  EINGVTQGDRLRALKSRRQSKTNAIPLT
          EINGVTQGDRLRALKS.RQSKTNAI.LT
Retrocopy EINGVTQGDRLRALKSQRQSKTNAILLT

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	13.38 RPM
SRP007412_cerebellum	0.00 RPM	9.97 RPM
SRP007412_heart	0.06 RPM	24.08 RPM
SRP007412_kidney	0.07 RPM	20.95 RPM
SRP007412_liver	0.09 RPM	28.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_208 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_208 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_208 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,