RetrogeneDB ID: retro_hsap_2807

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 3:82855664..82857188(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000241095
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CYP51A1
• Ensembl ID: ENSG00000001630
• Aliases: CYP51A1, CP51, CYP51, CYPL1, LDM, P450-14DM, P450L1
• Description: cytochrome P450, family 51, subfamily A, polypeptide 1 [Source:HGNC Symbol;Acc:2649]

Sequence

>retro_hsap_2807
ATGGCGGCGGCGGCCGGGATGATGCTGCTGGGCTTGCTACAGGCGGGTGGGTAGGTGCTGGGCCAGGCGATGGAGGAGGT
GGCAGGCGGCAACCTCTTGTCCATGCTGCTGATCGCCTGCGCCTTCACCCTCAGCCTGGTCTACTTGTTCCGTCTCGCTG
CCGGCCACCTGGTCCAGCTGACCGCAGGGGCGAAAAGTCCTCCGTACATTTTCTCCCCAGTTCCTTTCCTTGGGCATGCC
ATAGCATTTGGGAAAAGTCCAACTGAATTTCTAGAAAATGCATATGGGAATTATGGACCTGTATTTAGTTTTATCATGGT
AGGCAAGGCATTTACTTACCTTCTGGGTAGTGATGCTGCTGCACTGCTTTTTAATAGTAAAAATGAAGTCCTGAATGCAG
AAGATGTCTACAGTCGCCTGACAACACCTGTGTTTGGGTAGGGAGTTGCATACGATGTGCCTAATCCAGTTTTCTTGGAG
CAGAAGAAAACGTTAAAAAGTGGCCTTAATATAGCCCACTTTAAATAGCATGTTTCTATAATTGAAAAAGAAACAAAGGA
ATACTTTGAGAGTTGGGGAGAAAGTGGAGAAAAAAATGTGTTTGCAGCTCTTTCTGAGCTCATAATTTTAACAGCTAGCC
ATTATTTGCATGGAAAGGAAATCAGAAGTCAACACAATGAAAAGGTAGCACAGCTGTATGCAGATTTGGATGGAGGTTTC
AGCCATGCAGCCTGGCTCTTACCAGGTTGGCTGCCTTTGCCTAGTTTCAGACGCAGGGACAGAGCTCATCAGGAAATCAA
GGATATTTTCTATAAGGCAATCCAGAAACGCAGACAGTCTCAAGAAAAAATTGATGACATTCTCCAAACTTTACTAGATG
CTACATACAAGGATGGGCGTCCTTTGACTGATGATGAAGTAGCAGGGATGCTTACTGGATTACTCTTGGCAGAGCAGCAT
ACATCCTCAACTAGTGCTTAGATGGGCTTCTTTTTGGCCAGAGACAAAACACTTCAAGAAAAATGTTATTTAGAACAGAA
AACAGTCTGTGGAGAGAATCTGCCTCCTTTAACTTATGACCAGCTCAAGGATCTAAATTTACTTGATCGCTGTATAAAAG
AAACATTAAGACTTAGACATCCTGTAATGATCATGATGAGAATGGCCAGAATTCCTAAAACTGTGGCAGGGTATACCATT
CCTCCGGGACATCAGGTGTGTGTTTCTCCTACTGTCAATCAAAGACTTAAAGATTCATGGGTAGAACACCTGGACTTTAA
TCCTGATCGCTACTTATAGGATAACCCAGCATCAAGGGAAAAGTTTGCCTATGTGCCATTTGGAGCTGGGCATCATGGTT
GTACTGGGGAAAATTTTGCCTATGTTCAAATTAAGACAATTTGGTCCACTATGCTTCGTTTATATGAATTTGATCTCATT
GATGGATACTTTCCCACCGTGAATTATACAACTATGATTCACACCCCTGAAAACCCAGTTATCCATTACAAACGAAGATC
AAAA

Alignment

ORF - retro_hsap_2807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.73 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAAGMLLLGLLQAGGSVLGQAMEKVTGGNLLSMLLIACAFTLSLVYLIRLAAGHLVQLPAGVKSPPYI
          MAAAAGM.LLGLLQAGG.VLGQAME.V.GGNLLSMLLIACAFTLSLVYL.RLAAGHLVQL.AG.KSPPYI
Retrocopy MAAAAGMMLLGLLQAGG*VLGQAMEEVAGGNLLSMLLIACAFTLSLVYLFRLAAGHLVQLTAGAKSPPYI

Parental  FSPIPFLGHAIAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEDVYSRL
          FSP.PFLGHAIAFGKSP.EFLENAY..YGPVFSF.MVGK.FTYLLGSDAAALLFNSKNE.LNAEDVYSRL
Retrocopy FSPVPFLGHAIAFGKSPTEFLENAYGNYGPVFSFIMVGKAFTYLLGSDAAALLFNSKNEVLNAEDVYSRL

Parental  TTPVFGKGVAYDVPNPVFLEQKKMLKSGLNIAHFKQHVSIIEKETKEYFESWGESGEKNVFEALSELIIL
          TTPVFG.GVAYDVPNPVFLEQKK.LKSGLNIAHFK.HVSIIEKETKEYFESWGESGEKNVF.ALSELIIL
Retrocopy TTPVFG*GVAYDVPNPVFLEQKKTLKSGLNIAHFK*HVSIIEKETKEYFESWGESGEKNVFAALSELIIL

Parental  TASHCLHGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKDIFYKAIQKRRQS
          TASH.LHGKEIRSQ.NEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAH.EIKDIFYKAIQKRRQS
Retrocopy TASHYLHGKEIRSQHNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHQEIKDIFYKAIQKRRQS

Parental  QEKIDDILQTLLDATYKDGRPLTDDEVAGMLIGLLLAGQHTSSTTSAWMGFFLARDKTLQKKCYLEQKTV
          QEKIDDILQTLLDATYKDGRPLTDDEVAGML.GLLLA.QHTSS.TSA.MGFFLARDKTLQ.KCYLEQKTV
Retrocopy QEKIDDILQTLLDATYKDGRPLTDDEVAGMLTGLLLAEQHTSS-TSA*MGFFLARDKTLQEKCYLEQKTV

Parental  CGENLPPLTYDQLKDLNLLDRCIKETLRLRPPIMIMMRMARTPQTVAGYTIPPGHQVCVSPTVNQRLKDS
          CGENLPPLTYDQLKDLNLLDRCIKETLRLR.P.MIMMRMAR.P.TVAGYTIPPGHQVCVSPTVNQRLKDS
Retrocopy CGENLPPLTYDQLKDLNLLDRCIKETLRLRHPVMIMMRMARIPKTVAGYTIPPGHQVCVSPTVNQRLKDS

Parental  WVERLDFNPDRYLQDNPASGEKFAYVPFGAGRHRCIGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNY
          WVE.LDFNPDRYL.DNPAS.EKFAYVPFGAG.H.C.GENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNY
Retrocopy WVEHLDFNPDRYL*DNPASREKFAYVPFGAGHHGCTGENFAYVQIKTIWSTMLRLYEFDLIDGYFPTVNY

Parental  TTMIHTPENPVIRYKRRSK
          TTMIHTPENPVI.YKRRSK
Retrocopy TTMIHTPENPVIHYKRRSK

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	0.22 RPM	2.56 RPM
bodymap2_adrenal	0.00 RPM	1.17 RPM
bodymap2_brain	0.00 RPM	2.74 RPM
bodymap2_breast	0.00 RPM	1.42 RPM
bodymap2_colon	0.00 RPM	1.22 RPM
bodymap2_heart	0.02 RPM	0.52 RPM
bodymap2_kidney	0.02 RPM	2.13 RPM
bodymap2_liver	0.00 RPM	2.05 RPM
bodymap2_lung	0.02 RPM	2.14 RPM
bodymap2_lymph_node	0.02 RPM	1.21 RPM
bodymap2_ovary	0.04 RPM	5.42 RPM
bodymap2_prostate	0.00 RPM	1.20 RPM
bodymap2_skeletal_muscle	0.00 RPM	0.64 RPM
bodymap2_testis	0.06 RPM	5.67 RPM
bodymap2_thyroid	0.24 RPM	2.24 RPM
bodymap2_white_blood_cells	0.00 RPM	0.59 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_2807 was not detected

EST

No EST(s) were mapped for retro_hsap_2807 retrocopy.

TSS

No TSS is located nearby retro_hsap_2807 retrocopy 5' end.

Lab

retro_hsap_2807 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_2807 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1901
Gorilla gorilla	retro_ggor_1952

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005722	1 retrocopy	retro_amel_1512,
Homo sapiens	ENSG00000001630	2 retrocopies	retro_hsap_1248, retro_hsap_2807 ,
Loxodonta africana	ENSLAFG00000000066	1 retrocopy	retro_lafr_272,
Monodelphis domestica	ENSMODG00000010610	1 retrocopy	retro_mdom_436,
Pongo abelii	ENSPPYG00000017824	2 retrocopies	retro_pabe_1039, retro_pabe_1040,
Pan troglodytes	ENSPTRG00000019391	2 retrocopies	retro_ptro_1901, retro_ptro_859,
Tarsius syrichta	ENSTSYG00000014341	1 retrocopy	retro_tsyr_1008,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.02 RPM
CEU_NA11843	0.00 RPM
CEU_NA11930	0.16 RPM
CEU_NA12004	0.00 RPM
CEU_NA12400	0.00 RPM
CEU_NA12751	0.00 RPM
CEU_NA12760	0.04 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.03 RPM
CEU_NA12873	0.03 RPM
FIN_HG00183	0.05 RPM
FIN_HG00277	0.15 RPM
FIN_HG00315	0.00 RPM
FIN_HG00321	0.06 RPM
FIN_HG00328	0.05 RPM
FIN_HG00338	0.00 RPM
FIN_HG00349	0.03 RPM
FIN_HG00375	0.02 RPM
FIN_HG00377	0.00 RPM
FIN_HG00378	0.02 RPM
GBR_HG00099	0.00 RPM
GBR_HG00111	0.02 RPM
GBR_HG00114	0.03 RPM
GBR_HG00119	0.05 RPM
GBR_HG00131	0.06 RPM
GBR_HG00133	0.05 RPM
GBR_HG00134	0.02 RPM
GBR_HG00137	0.00 RPM
GBR_HG00142	0.03 RPM
GBR_HG00143	0.00 RPM
TSI_NA20512	0.03 RPM
TSI_NA20513	0.02 RPM
TSI_NA20518	0.14 RPM
TSI_NA20532	0.00 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.09 RPM
TSI_NA20765	0.04 RPM
TSI_NA20771	0.06 RPM
TSI_NA20786	0.05 RPM
TSI_NA20798	0.03 RPM
YRI_NA18870	0.00 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.04 RPM
YRI_NA19093	0.03 RPM
YRI_NA19099	0.03 RPM
YRI_NA19114	0.00 RPM
YRI_NA19118	0.04 RPM
YRI_NA19213	0.02 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.06 RPM

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Indel association:

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