RetrogeneDB ID: retro_hsap_101

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 4:41983809..41985000(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000182308
• Aliases: DCAF4L1, WDR21B
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DCAF4
• Ensembl ID: ENSG00000119599
• Aliases: DCAF4, WDR21, WDR21A
• Description: DDB1 and CUL4 associated factor 4 [Source:HGNC Symbol;Acc:20229]

Sequence

>retro_hsap_101
ATGGAGGCTGAAAGGCTGCGACTCCTCGAGGAAGAGGCCAAGCTGAAAAAGGTAGCCAGAATGGGATTTAATGCATCTTC
CATGCTCCGAAAAAGCCAGCTAGGTTTCCTCAACGTCACCAGTTACTCCCGTTTAGCCAACGAGCTGCGTGTGAGCTGCA
TGGAGCGGAAAAAGGTCCAAATTCGGAGCTTGGATCCCTCCTCTTTGGCGAGCGACCGATTTAACTTCATTCTGGCGAGT
ACCAACAGCGACCAGCTCTTCGTAGTGAACCAGGTCGAAGTCGAAGGCTCCAAGTACGGCATCATCAGCCTGCGAACTCT
GAAGATCCCTTCGTTCCACGTGTACGTGCTCAGAAACCTCTACGTCCCCAACCGGAAGGTGAAGTCCCTGTGCTGGGCCT
CGCTGAACCAGTTGGACTCTCACGTTCTGCTGTGCTTCGAGGGAATCACAGATGCTCCAAGCTGTGCAGTGCTGCTCCCA
GCGTCGCGGTTCTTAAGTGTTCACACAAGAGTTAACCAGCCTGGCATGCTCTGCAGTTTCCAGATCCCAGAGGCCTGGTC
CTGTGCGTGGTCCCTCAACACCCGGGCATATCACTGCTTTAGTGCAGGCTTGTCTCAGCAGGTCCTGTTGACCAGCGTGG
CGACGGGACACCAGCAGTCATTTGATACCAGCAGTGATGTCTTGGCCCAGCAGTTTGCTAGTACGGCTCCTTTGCTGTTT
AATGGCTGTCGCTCCGGGGAGATCTTTGCCATTGATCTGCGTTGTAGAAATCGAGGCAAGGGGTGGAGGGCCACTCGCCT
GTTCCATGACTCAGCAGTGACCTCTGTGCAAATCCTCCAAGAAGAGCAATGCCTGATGGCATCAGACATGACTGGAAAGA
TCAAGCTGTGGGATCTGAGGGCCACTAAATGTGTAAGGCAGTACGAAGGTCACGTGAATGAGTCCGCCTATCTGCCCCTG
CATGTGCACGAGGAAGAGGGAATCGTGGTGGCAGTGGGCCAGGACTGCTACACGAGAATCTGGAGCCTCCATGATGCCCA
CCTGCTCAGAACCATCCCTTCCCCGTACTCTGCCTCCGAGGACGACATTCCCAGCGTGGCCTTCGCTTCTCGGCTCGGGG
GCATCCGGGGAGCAGCACCAGGGCTGCTCATGGCTGTCCGGCAGGACCTTTATTGTTTCCCCTTCAGCTAA

Alignment

ORF - retro_hsap_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 79.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESKRLRLLQEEDRRKKIARMGFNASSMLRKSQLGFLNVTNYCHLAHELRLSCMERKKVQIRSMDPSALA
          ME..RLRLL.EE...KK.ARMGFNASSMLRKSQLGFLNVT.Y..LA.ELR.SCMERKKVQIRS.DPS.LA
Retrocopy MEAERLRLLEEEAKLKKVARMGFNASSMLRKSQLGFLNVTSYSRLANELRVSCMERKKVQIRSLDPSSLA

Parental  SDRFNLILADTNSDRLFTVNDVKVGGSKYGIINLQSLKTPTLKVFMHENLYFTNRKVNSVCWASLNHLDS
          SDRFN.ILA.TNSD.LF.VN.V.V.GSKYGII.L..LK.P...V....NLY..NRKV.S.CWASLN.LDS
Retrocopy SDRFNFILASTNSDQLFVVNQVEVEGSKYGIISLRTLKIPSFHVYVLRNLYVPNRKVKSLCWASLNQLDS

Parental  HILLCLMGLAETPGCATLLPASLFVNSHPGIDRPGMLCSFRIPGAWSCAWSLNIQANNCFSTGLSRRVLL
          H.LLC..G....P.CA.LLPAS.F...H.....PGMLCSF.IP.AWSCAWSLN..A..CFS.GLS..VLL
Retrocopy HVLLCFEGITDAPSCAVLLPASRFLSVHTRVNQPGMLCSFQIPEAWSCAWSLNTRAYHCFSAGLSQQVLL

Parental  TNVVTGHRQSFGTNSDVLAQQFALMAPLLFNGCRSGEIFAIDLRCGNQGKGWKATRLFHDSAVTSVRILQ
          T.V.TGH.QSF.T.SDVLAQQFA..APLLFNGCRSGEIFAIDLRC.N.GKGW.ATRLFHDSAVTSV.ILQ
Retrocopy TSVATGHQQSFDTSSDVLAQQFASTAPLLFNGCRSGEIFAIDLRCRNRGKGWRATRLFHDSAVTSVQILQ

Parental  DEQYLMASDMAGKIKLWDLRTTKCVRQYEGHVNEYAYLPLHVHEEEGILVAVGQDCYTRIWSLHDARLLR
          .EQ.LMASDM.GKIKLWDLR.TKCVRQYEGHVNE.AYLPLHVHEEEGI.VAVGQDCYTRIWSLHDA.LLR
Retrocopy EEQCLMASDMTGKIKLWDLRATKCVRQYEGHVNESAYLPLHVHEEEGIVVAVGQDCYTRIWSLHDAHLLR

Parental  TIPSPYPASKADIPSVAFSSRLGGSRG-APGLLMAVGQDLYCYSYS
          TIPSPY.AS..DIPSVAF.SRLGG.RG.APGLLMAV.QDLYC...S
Retrocopy TIPSPYSASEDDIPSVAFASRLGGIRGAAPGLLMAVRQDLYCFPFS

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	0.18 RPM	6.06 RPM
bodymap2_adrenal	0.00 RPM	16.95 RPM
bodymap2_brain	0.05 RPM	7.81 RPM
bodymap2_breast	0.00 RPM	9.14 RPM
bodymap2_colon	0.00 RPM	4.66 RPM
bodymap2_heart	0.13 RPM	2.27 RPM
bodymap2_kidney	0.29 RPM	9.27 RPM
bodymap2_liver	0.00 RPM	4.06 RPM
bodymap2_lung	0.11 RPM	4.83 RPM
bodymap2_lymph_node	0.37 RPM	5.57 RPM
bodymap2_ovary	0.00 RPM	14.11 RPM
bodymap2_prostate	0.07 RPM	8.56 RPM
bodymap2_skeletal_muscle	0.27 RPM	7.51 RPM
bodymap2_testis	12.50 RPM	15.52 RPM
bodymap2_thyroid	0.13 RPM	21.43 RPM
bodymap2_white_blood_cells	0.00 RPM	5.06 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_101 was not detected

EST

12 EST(s) were mapped to retro_hsap_101 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DB061825	41983794	41984345	99.9	550	1	549
DB073896	41983848	41984389	99.3	540	1	538
DB077714	41983791	41984363	100	572	0	572
DB080353	41983772	41984294	100	522	0	522
DB088066	41983790	41984347	97.9	550	7	541
DB093013	41983791	41984341	99.9	549	1	548
DB095626	41983791	41984356	99.9	564	1	563
DB100231	41983712	41984285	99.9	572	1	571
DB448052	41983848	41984276	99.8	426	1	424
HY001456	41983801	41984320	99.7	517	2	515
HY026379	41983801	41984235	99.6	432	2	430
HY053415	41983939	41984503	99.5	557	3	554

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_143956	1806 libraries	20 libraries	0 libraries	0 libraries	3 libraries

The graphical summary, for retro_hsap_101 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_101 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_101 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_46
Gorilla gorilla	retro_ggor_2026
Macaca mulatta	retro_mmul_152

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013878	1 retrocopy	retro_cpor_293,
Homo sapiens	ENSG00000119599	2 retrocopies	retro_hsap_101 , retro_hsap_92,
Gorilla gorilla	ENSGGOG00000003815	2 retrocopies	retro_ggor_2026, retro_ggor_2743,
Macaca mulatta	ENSMMUG00000003625	2 retrocopies	retro_mmul_152, retro_mmul_264,
Nomascus leucogenys	ENSNLEG00000002449	2 retrocopies	retro_nleu_1912, retro_nleu_833,
Pan troglodytes	ENSPTRG00000006507	2 retrocopies	retro_ptro_2774, retro_ptro_46,