RetrogeneDB ID: retro_hsap_3729

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:48964181..48965630(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000218305
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CDC14B
• Ensembl ID: ENSG00000081377
• Aliases: CDC14B, CDC14B3, Cdc14B1, Cdc14B2, hCDC14B
• Description: cell division cycle 14B [Source:HGNC Symbol;Acc:1719]

Sequence

>retro_hsap_3729
AAGCGGAAAAGCAAGGGGCGGTCGAGCTGGGCCGCCGCGCCCCACTGCTCGCCGCGCTGCTCTTTGACCTCGCAGGGTGT
GAAGAAGATGCGCAGCTCCACGCTGCAGGACCCGCGCCGCCGGGACCCCCAGGACGACGTGTACGTGGACATCACCGATC
GCCTTCGTTTTGCCATTCTCTACAGCAGACCAAAGAGTGCATCAAATGTACATTATTTCAGCATAGATAATGAACTCGAA
TATGAGAACTTCTCCGAAGACTTTGGACCACTCAATCTGGCAATGGTTTACAGATATTGTTGCAAGATAAATAAGAAATT
AAAGTCCATTACAATGTTAAGGAAGAAAATTGTTCATTTTACTGGCTCTGATCAGAGAAAACAAGCAAATGCTGCCTTCC
TTGTTGGATGCTACATGGTTATATACTTGGGGAGAACCCCAGAAGCAGCATATAGAATATTAATCTTTGGAGATACACCC
TATATTCCTTTCAGAGATGCTGCCTATGGAAGCTGCAATTTCTACATTACACTTCTTGACTGTTTTCATGCAGTAAAGAA
GGCAATGCAGTATGGCTTCCTTAATTTCAACTCATTTAACCTTGATGAATATGAACACTATGAAAAAGCAGAAAACGGAG
ATTTAAATTGGATAATACCAGACCGATTTATTGCCTTCTGTGGACCTCATTCAAGAGCCAGACTTGAAAGTGGTTACCAC
CAACATTCTCCCGAGACTTATATTCAATATTTTAAGAATCACAATGTTACTACCATTATTCGTCTGAATAAAAGGATGTA
TGATGCCAAACGCTTTACGGATGCTGGCTTCGATCACCATGATCTTTTCTTTGCGGATGGCAGCACCCCTACTGATGCCA
TTGTCAAAAGATTTCTGGATATCTGTGAAAATGCTGAGGGTGCCATTGCAGTACATTGTAAAGCTGGCCTTGGTCGCACA
GGCACTCTGATAGCCTGCTACATCATGAAGCATTACAGGATGACAGCAGCCGAGACCATTGCGTGGGTAAGGATCTGCAG
ACCTGGCTTGGTGATCGGGCCTCAGCAGCAGTTTTTGGTGATGAAGCAAACAAGCCTCTGGCTGGAAGGGGACTATTTTC
GTCAGAGGTTAAAGGGGCAGGAGAATGGACAACACAGAGCAGCCTTCTCCAAACTTCTCTCTGGTGTTGATGACATTTCC
ATAAATGGGGTCGAGAATCAAGACCAGCAAGAACCCAAACCTTACAGTGATGACGACGAAATCAATGGAGTGACACAAGG
TGATAGAAGTCGGGCCCTGAAAAGGCGAAGACAATCAAAAACAAACGATATTCTTCTCCCATCTCCCCTGGCTGTGCTGA
CCTTTACACTGTGTAGTGTTGTCATCTGGTGGATTGTTTGTGACTACATTCTTCCCATCCTGCTATTCTGACTCAAAGAT
TTCAGAACA

Alignment

ORF - retro_hsap_3729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.58 %
• Parental protein coverage: 99.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRKSERRSSWAAAPPCSRRCSSTSPGVKKIRSSTQQDPRRRDPQDDVYLDITDRLCFAILYSRPKSASNV
          KRKS..RSSWAAAP.CS.RCS.TS.GVKK.RSST.QDPRRRDPQDDVY.DITDRL.FAILYSRPKSASNV
Retrocopy KRKSKGRSSWAAAPHCSPRCSLTSQGVKKMRSSTLQDPRRRDPQDDVYVDITDRLRFAILYSRPKSASNV

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.LWLEGDYFRQ.LKGQENGQHRAAFSKLLSGVDDISINGVENQDQQEP.PYSDDDE
Retrocopy VIGPQQQFLVMKQTSLWLEGDYFRQRLKGQENGQHRAAFSKLLSGVDDISINGVENQDQQEPKPYSDDDE

Parental  INGVTQGDRLRALKSRRQSKTNAIPLTCPLAVLTSALCSVVIWWIVCDYILPILLFCLDGFRT
          INGVTQGDR.RALK.RRQSKTN.I.L..PLAVLT..LCSVVIWWIVCDYILPILLF.L..FRT
Retrocopy INGVTQGDRSRALKRRRQSKTNDILLPSPLAVLTFTLCSVVIWWIVCDYILPILLF*LKDFRT

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
bodymap2_adipose	0.00 RPM	39.82 RPM
bodymap2_adrenal	0.00 RPM	16.44 RPM
bodymap2_brain	0.00 RPM	41.11 RPM
bodymap2_breast	0.00 RPM	41.69 RPM
bodymap2_colon	0.00 RPM	21.04 RPM
bodymap2_heart	0.00 RPM	28.23 RPM
bodymap2_kidney	0.00 RPM	31.23 RPM
bodymap2_liver	0.00 RPM	39.04 RPM
bodymap2_lung	0.00 RPM	18.57 RPM
bodymap2_lymph_node	0.04 RPM	26.57 RPM
bodymap2_ovary	0.02 RPM	25.99 RPM
bodymap2_prostate	0.00 RPM	39.52 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.04 RPM
bodymap2_testis	2.38 RPM	44.83 RPM
bodymap2_thyroid	0.13 RPM	52.99 RPM
bodymap2_white_blood_cells	0.00 RPM	23.13 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_3729 was not detected

EST

8 EST(s) were mapped to retro_hsap_3729 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG722222	48964156	48964742	99.4	581	4	576
BG723382	48964168	48964891	99.5	718	4	713
DB070746	48964178	48964727	99.9	548	0	546
HY001658	48964136	48964614	99.6	476	2	474
HY023564	48964169	48964639	99.8	468	1	467
HY025565	48964168	48964653	99.8	482	1	481
HY042625	48964158	48964428	98.2	264	5	259
HY053609	48964124	48964618	99	487	5	481

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_176110	1826 libraries	0 libraries	2 libraries	1 library	0 libraries

The graphical summary, for retro_hsap_3729 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_hsap_3729 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3729 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,