RetrogeneDB ID: retro_hsap_3845

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 7:48885997..48886897(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000225705
• 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_3845
GCAGTAAAGAAGGCAATGCAGTATGGCTTCCTTAATTTCAACTCATTTAACCTTGATGAATATGAACACTATGAAAAAGC
AGAAAACGGAGATTTAAATTGGCTAATACCAGACCGATTTATTGCCTTCTGTGGACCTCATTCAAGAGCCAGACTTGAAA
GTGGTTACCACCAACATTCTCCCGAGACTTATATTCAATATTTTAAGAATCACAATGTTACTACCATTATTCGTCTGAAT
AAAAGGATACATGATGCCAAACGCTTTACGGATGCTGGCTTCGATCACCATGATCTTTTCTTTGCAGATGGCAGCACCCC
TACTGATGCCATTGTCAAAAGATTTCTGGATATCTGTGAAAATGCTGAGGGTGCCATTGCAGTACATTGTAAAGCTGGCC
TTGGTCGCACAGGCACTCTGATAGCCTGCTACATCATGAAGCATTACAGGATGACAGCAGCCGAGACCATTGCGTGGGTA
AGGATCTGCAGACCTGGCTTGGTGATCGGGCCTCCGCAGCAGTTTTTGGTGATGAAGCAAACAAGCCTCTGGCTGGAAGG
GGACTATTTTCGTCAGAAGTTAAAGGGGCAGGAGAATGGACAACACAGAGCAGCCTTCTCCAAACTTCTCTCTGGTGTTG
ATGACATTTCCATAAATGGGGTCGAGAATCAAGACCAGCAAGAACCCAAACCTTACGGTGATGACGACGAAATCAATGGA
GTGACACAAGGTGATAGAAGTCGGGCCCTGAAAAGGCAAAGACAATCAAAAACAAACGATATTCTTCTCCCATCTCCCCT
GGCTGTGCTGACCTTTACACTGTGTAGTGTTGTCATCTGGTGGATTGTTTGTGACTACATTCTTCCCATCCTGCTATCCT
GACTCGAAGATTTCAGAACA

Alignment

ORF - retro_hsap_3845 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.67 %
• Parental protein coverage: 61.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AVKKAMQYGFLNFNSFNLDEYEHYEKAENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKN
          AVKKAMQYGFLNFNSFNLDEYEHYEKAENGDLNW.IPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKN
Retrocopy AVKKAMQYGFLNFNSFNLDEYEHYEKAENGDLNWLIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKN

Parental  HNVTTIIRLNKRMYDAKRFTDAGFDHHDLFFADGSTPTDAIVKEFLDICENAEGAIAVHCKAGLGRTGTL
          HNVTTIIRLNKR..DAKRFTDAGFDHHDLFFADGSTPTDAIVK.FLDICENAEGAIAVHCKAGLGRTGTL
Retrocopy HNVTTIIRLNKRIHDAKRFTDAGFDHHDLFFADGSTPTDAIVKRFLDICENAEGAIAVHCKAGLGRTGTL

Parental  IACYIMKHYRMTAAETIAWVRICRPGSVIGPQQQFLVMKQTNLWLEGDYFRQKLKGQENGQHRAAFSKLL
          IACYIMKHYRMTAAETIAWVRICRPG.VIGP.QQFLVMKQT.LWLEGDYFRQKLKGQENGQHRAAFSKLL
Retrocopy IACYIMKHYRMTAAETIAWVRICRPGLVIGPPQQFLVMKQTSLWLEGDYFRQKLKGQENGQHRAAFSKLL

Parental  SGVDDISINGVENQDQQEPEPYSDDDEINGVTQGDRLRALKSRRQSKTNAIPLTCPLAVLTSALCSVVIW
          SGVDDISINGVENQDQQEP.PY.DDDEINGVTQGDR.RALK..RQSKTN.I.L..PLAVLT..LCSVVIW
Retrocopy SGVDDISINGVENQDQQEPKPYGDDDEINGVTQGDRSRALKRQRQSKTNDILLPSPLAVLTFTLCSVVIW

Parental  WIVCDYILPILLFCLDGFRT
          WIVCDYILPILL..L..FRT
Retrocopy WIVCDYILPILLS*LEDFRT

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	0.09 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	0.00 RPM	26.57 RPM
bodymap2_ovary	0.00 RPM	25.99 RPM
bodymap2_prostate	0.00 RPM	39.52 RPM
bodymap2_skeletal_muscle	0.00 RPM	7.04 RPM
bodymap2_testis	0.68 RPM	44.83 RPM
bodymap2_thyroid	0.00 RPM	52.99 RPM
bodymap2_white_blood_cells	0.00 RPM	23.13 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_3845 was not detected

EST

No EST(s) were mapped for retro_hsap_3845 retrocopy.

TSS

No TSS is located nearby retro_hsap_3845 retrocopy 5' end.

Lab

retro_hsap_3845 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_3845 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2621

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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,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.00 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.00 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.00 RPM
CEU_NA12827	0.00 RPM
CEU_NA12872	0.00 RPM
CEU_NA12873	0.00 RPM
FIN_HG00183	0.00 RPM
FIN_HG00277	0.00 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.00 RPM
FIN_HG00328	0.00 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.00 RPM
FIN_HG00375	0.00 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.00 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.00 RPM
GBR_HG00114	0.00 RPM
GBR_HG00119	0.00 RPM
GBR_HG00131	0.00 RPM
GBR_HG00133	0.02 RPM
GBR_HG00134	0.00 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.00 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.00 RPM
TSI_NA20513	0.00 RPM
TSI_NA20518	0.00 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.00 RPM
TSI_NA20756	0.00 RPM
TSI_NA20765	0.00 RPM
TSI_NA20771	0.00 RPM
TSI_NA20786	0.00 RPM
TSI_NA20798	0.00 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.00 RPM
YRI_NA19093	0.00 RPM
YRI_NA19099	0.00 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.00 RPM
YRI_NA19213	0.00 RPM
YRI_NA19214	0.00 RPM
YRI_NA19223	0.00 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).