RetrogeneDB ID: retro_hsap_604

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 10:88768013..88769653(+)
• Located in intron of: ENSG00000272508

Retrocopy information

• Ensembl ID: ENSG00000261011
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AGAP1
• Ensembl ID: ENSG00000157985
• Aliases: AGAP1, AGAP-1, CENTG2, GGAP1, cnt-g2
• Description: ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 [Source:HGNC Symbol;Acc:16922]

Sequence

>retro_hsap_604
AGAAAATGTATCTTTTTAAAAGGTAATTGTGAGCTGTCTATAGGACCCTGCAAGCCACTACCCAATTTTTGAAGCCATTC
TTCTTCTGTTCCACACAGTTTTCCACCGTGCACATTACGAAGAAAAGAAATGGAGGTGGGAGTTTAAATAACTATTCCTC
CTCCATTCCATTGACTCCCAGCACCAGCCAGGAGGACCTTTATTTCAGTGTTCCTCCCACTGCCAACACACCCACGCCCA
TTTGCAAGCAGTCCATGGGCTGGTCCAACCTGTTTACATCTGAGAAAGGGAGTGACCCAGACAAAGGGAGGAAAGCCCTG
GAGAGTCACGCTGACACCATCGGGAGCGGCAGAGCCATCCCCATTAAACAGGGCATGCTCTTAAAGCGAAGTGGGAAATG
GCTGAAGACATGGAAAAAGAAATATGTCACCCTGTGTTCCAATGGCGTGCTCACCTATTATTCAAGCTTAGGTGATTATA
TGAAGAATATTCATAAAAAAGAGATTGACCTTCGGACATCTACCATCAAAGTCCCAGGAAAGTGGCCATCCCTAGCCACA
TCGGCCTGCGCACCCATCTCCAGCTCTAAAAGCAATGGCCTATCCAAGGACATGGAAGCTCTGCATATGTCAGCCAATTC
AGACATCGGGCTGGGTGACTCCATATGCTTCAGCCCCAGTATCTCCAGCACCACCAGCCCCAAGCTCAACCTGCCCCCCT
CCCCTCATGCCAATAAAAAGAAACACCTAAAGAAGAAAAGCACCAACAACTTAAAAGATGATGGCCTGTCCAGCACTGCT
GAGGAAGAAGAAGAAAAGTTTATGATTGTGTCCGTCACTGGCCAAACGTGCCACTTTAAAGCCACGACGTATGAGGAGCG
GGATGCCTGGGTCCAAGCCATCCAGAGCCAGATCCTGGCCAGCCTGCAGTCATGCGAGAGCAGTAAAAGCAAGTCCCAGC
TGACCAGCCAGAGTGAGGCCATGGCCCTGCAGTCGATCCAAAACATGCGTGGGAACTCCCACTGCGTGGACTGTGAGACC
CAGAATCCTAAGTGGGCCAGTTTGAACTTGGGAGTCCTCATGTGTATTGAATGTTCAGGAATCCACCGCAGTCTTGGCAC
CCGCCTTTCCCGTGTGCGATCTCTGGAGCTGGATGACTGGCCAGTTGAGCTCAGGAAGGTTATGTCATCTATTGGCAATG
ACCTAGCCAACAGCATCTGGGAAGGGAGCAGCCAGGGGCAGACGAAACCCTCAATAGAGTCAACGAGGGAAGAGAAGGAA
CGGTGGATCCGTTCCAAATATGAGCATAAGCTCTTTCTGGCCCCACTACCCTGCACTGAGCTGTCCCTGGGCCAGCACCT
GCTGCGGGCCACCGCTGATGAGGACCTGCGGACAGCCATCCTGCTGCTGGCACATGGCTCCCGTGAGGAGGTGAACGAGA
CCTGTGGGGAGGGAGACGGCTGCACGGCGCTCCATCTGGCCTGCCGCAAGGGGAATGTGGTCCTGGCGCAGCTCCTGATC
TGGTACGGGGTGGACGTCATGGCCCGAGATGCCCACGGGAACACAGCGCTGACCTACGCCCGGCAGGCCTCCAGCCAGGA
GTGCATCAACGTGCTTCTGCAGTACGGCTGCCCCGACGAG

Alignment

ORF - retro_hsap_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.4 %
• Parental protein coverage: 51.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QKIVATRKKQQLSIGPCKSLPNSPSHSS-VCSAQVSAVHISQTSNGGGSLSDYSSSVPSTPSTSQKELRI
          .K.........LSIGPCK.LPN..SHSS..CS.Q.S.VHI....NGGGSL..YSSS.P.TPSTSQ..L..
Retrocopy RKCIFLKGNCELSIGPCKPLPNF*SHSS<FCSTQFSTVHITKKRNGGGSLNNYSSSIPLTPSTSQEDLYF

Parental  DVPPTANTPTPVRKQSKRRSNLFTSRKGSDPDKEKKGLESRADSIGSGRAIPIKQGMLLKRSGKSLNKEW
          .VPPTANTPTP..KQS...SNLFTS.KGSDPDK..K.LES.AD.IGSGRAIPIKQGMLLKRSGK.L.K.W
Retrocopy SVPPTANTPTPICKQSMGWSNLFTSEKGSDPDKGRKALESHADTIGSGRAIPIKQGMLLKRSGKWL-KTW

Parental  KKKYVTLCDNGVLTYHPSLHDYMQNVHGKEIDLLRTTVKVPGKRPPRATSACAPISSPKTNGLSKDMSSL
          KKKYVTLC.NGVLTY..SL.DYM.N.H.KEIDL...T.KVPGK.P..ATSACAPISS.K.NGLSKDM..L
Retrocopy KKKYVTLCSNGVLTYYSSLGDYMKNIHKKEIDLRTSTIKVPGKWPSLATSACAPISSSKSNGLSKDMEAL

Parental  HISPNSDTGLGDSVCSSPSISSTTSPKLDPPPSPHANRKKHRRKKSTSNFKADGLSGTAEEQEENFEFII
          H.S.NSD.GLGDS.C.SPSISSTTSPKL..PPSPHAN.KKH..KKST.N.K.DGLS.TAEE.EE...F.I
Retrocopy HMSANSDIGLGDSICFSPSISSTTSPKLNLPPSPHANKKKHLKKKSTNNLKDDGLSSTAEEEEE--KFMI

Parental  VSLTGQTWHFEATTYEERDAWVQAIESQILASLQSCESSKNKSRLTSQSEAMALQSIRNMRGNSHCVDCE
          VS.TGQT.HF.ATTYEERDAWVQAI.SQILASLQSCESSK.KS.LTSQSEAMALQSI.NMRGNSHCVDCE
Retrocopy VSVTGQTCHFKATTYEERDAWVQAIQSQILASLQSCESSKSKSQLTSQSEAMALQSIQNMRGNSHCVDCE

Parental  TQNPNWASLNLGALMCIECSGIHRNLGTHLSRVRSLDLDDWPVELIKVMSSIGNELANSVWEESSQGRTK
          TQNP.WASLNLG.LMCIECSGIHR.LGT.LSRVRSL.LDDWPVEL.KVMSSIGN.LANS.WE.SSQG.TK
Retrocopy TQNPKWASLNLGVLMCIECSGIHRSLGTRLSRVRSLELDDWPVELRKVMSSIGNDLANSIWEGSSQGQTK

Parental  PSVDSTREEKERWIRAKYEQKLFLAPLPCTELSLGQHLLRATADEDLRTAILLLAHGSRDEVNETCGEGD
          PS..STREEKERWIR.KYE.KLFLAPLPCTELSLGQHLLRATADEDLRTAILLLAHGSR.EVNETCGEGD
Retrocopy PSIESTREEKERWIRSKYEHKLFLAPLPCTELSLGQHLLRATADEDLRTAILLLAHGSREEVNETCGEGD

Parental  GRTALHLACRKGNVVLAQLLIWYGVDVTARDAHGNTALAYARQASSQECIDVLLQYGCPDE
          G.TALHLACRKGNVVLAQLLIWYGVDV.ARDAHGNTAL.YARQASSQECI.VLLQYGCPDE
Retrocopy GCTALHLACRKGNVVLAQLLIWYGVDVMARDAHGNTALTYARQASSQECINVLLQYGCPDE

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	4.73 RPM	20.55 RPM
bodymap2_adrenal	2.58 RPM	12.94 RPM
bodymap2_brain	0.94 RPM	75.45 RPM
bodymap2_breast	4.61 RPM	16.60 RPM
bodymap2_colon	0.87 RPM	28.00 RPM
bodymap2_heart	1.02 RPM	17.78 RPM
bodymap2_kidney	1.28 RPM	12.37 RPM
bodymap2_liver	0.00 RPM	7.31 RPM
bodymap2_lung	3.18 RPM	13.73 RPM
bodymap2_lymph_node	1.17 RPM	9.87 RPM
bodymap2_ovary	5.51 RPM	13.40 RPM
bodymap2_prostate	6.84 RPM	15.31 RPM
bodymap2_skeletal_muscle	0.40 RPM	14.95 RPM
bodymap2_testis	2.56 RPM	22.02 RPM
bodymap2_thyroid	1.54 RPM	20.70 RPM
bodymap2_white_blood_cells	0.00 RPM	4.51 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_604 was not detected

EST

3 EST(s) were mapped to retro_hsap_604 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI659151	88768350	88768749	99	398	1	396
BF855622	88768193	88768679	97.4	478	7	467
DB333153	88768201	88768744	99.5	540	3	537

TSS

No TSS is located nearby retro_hsap_604 retrocopy 5' end.

Lab

retro_hsap_604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000157985	1 retrocopy	retro_hsap_604 ,
Macaca mulatta	ENSMMUG00000009346	1 retrocopy	retro_mmul_2398,
Nomascus leucogenys	ENSNLEG00000008562	1 retrocopy	retro_nleu_1923,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.17 RPM
CEU_NA11843	0.23 RPM
CEU_NA11930	0.29 RPM
CEU_NA12004	0.04 RPM
CEU_NA12400	0.11 RPM
CEU_NA12751	0.07 RPM
CEU_NA12760	0.22 RPM
CEU_NA12827	0.05 RPM
CEU_NA12872	0.16 RPM
CEU_NA12873	0.19 RPM
FIN_HG00183	0.22 RPM
FIN_HG00277	0.41 RPM
FIN_HG00315	0.14 RPM
FIN_HG00321	0.24 RPM
FIN_HG00328	0.09 RPM
FIN_HG00338	0.11 RPM
FIN_HG00349	0.06 RPM
FIN_HG00375	0.05 RPM
FIN_HG00377	0.10 RPM
FIN_HG00378	0.15 RPM
GBR_HG00099	0.09 RPM
GBR_HG00111	0.11 RPM
GBR_HG00114	0.21 RPM
GBR_HG00119	0.31 RPM
GBR_HG00131	0.09 RPM
GBR_HG00133	0.22 RPM
GBR_HG00134	0.17 RPM
GBR_HG00137	0.11 RPM
GBR_HG00142	0.17 RPM
GBR_HG00143	0.10 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.15 RPM
TSI_NA20518	0.14 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.05 RPM
TSI_NA20756	0.15 RPM
TSI_NA20765	0.06 RPM
TSI_NA20771	0.09 RPM
TSI_NA20786	0.21 RPM
TSI_NA20798	0.25 RPM
YRI_NA18870	0.07 RPM
YRI_NA18907	0.24 RPM
YRI_NA18916	0.08 RPM
YRI_NA19093	0.08 RPM
YRI_NA19099	0.24 RPM
YRI_NA19114	0.03 RPM
YRI_NA19118	0.12 RPM
YRI_NA19213	0.22 RPM
YRI_NA19214	0.15 RPM
YRI_NA19223	0.02 RPM

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Indel association:

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