RetrogeneDB ID:

retro_hsap_3742

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:64043110..64043586(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000224669
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GCSH
Ensembl ID:ENSG00000140905
Aliases:GCSH, GCE, NKH
Description:glycine cleavage system protein H (aminomethyl carrier) [Source:HGNC Symbol;Acc:4208]


Retrocopy-Parental alignment summary:






>retro_hsap_3742
ACCCTTCACGCGGCCCTGTCACCCGCCGCGCCCTGCCCGCCGAGGCCCTGGCAGCTGGGGGGTGGGCGCTGTTCGGACGC
TGCGCGCGGGACCACCTCTGCTCTCGGTGCGTAAATTCACAGAGAAACATGAATGGATGGCAACAGAAAATGATATTGGA
ACACTGGGAGTCAGCAGTTTTGCACAGGAAACGTTGGGAGATATTGTTTACTGTAGTCTGCCTGAAGTTGGGACAAAAGA
ACAAACAAGATGAGTTTGGTGCTTTGGAAAGTGTGAAAGCTGCTAGTGAACTCTATTCTCCTTTATCAGGAGAAGTAACT
TAAATTAATGAAGCTCTTGGAGAAAATCCAGGACTTGTAAACAAATCTTGTTATGAAGATGGTTGGCTGATCAAGATGAC
ACTAAGTAACCCTTCAGAACTAGATGAACTTATGAGTGAAGAAGTATATGAGAGATAGAGAAAATCTATTGAGGAG

ORF - retro_hsap_3742 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.71 %
Parental protein coverage: 91.91 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTLRAVPSPAAPCPPRPWQLG-VGAVRTLRTGPALLSVRKFTEKHEWVTTENGIGTVGISNFAQEALGDVV
TL.A..SPAAPCPPRPWQLG.VGAVRTLR.GP.LLSVRKFTEKHEW..TEN.IGT.G.S.FAQE.LGD.V
RetrocopyTLHAALSPAAPCPPRPWQLG>VGAVRTLRAGPPLLSVRKFTEKHEWMATENDIGTLGVSSFAQETLGDIV
ParentalYCSLPEV-GTKLNKQDEFGALESVKAASELYSPLSGEVTEINEALAENPGLVNKSCYEDGWLIKMTLSNP
YCSLPEV.G.K.NKQDEFGALESVKAASELYSPLSGEVT.INEAL.ENPGLVNKSCYEDGWLIKMTLSNP
RetrocopyYCSLPEV>GQK-NKQDEFGALESVKAASELYSPLSGEVT*INEALGENPGLVNKSCYEDGWLIKMTLSNP
ParentalSELDELMSEEAYEKYIKSIEE
SELDELMSEE.YE...KSIEE
RetrocopySELDELMSEEVYER*RKSIEE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
bodymap2_adipose 0 .02 RPM 1 .37 RPM
bodymap2_adrenal 0 .00 RPM 2 .35 RPM
bodymap2_brain 0 .00 RPM 6 .63 RPM
bodymap2_breast 0 .00 RPM 5 .35 RPM
bodymap2_colon 0 .00 RPM 1 .57 RPM
bodymap2_heart 0 .00 RPM 2 .53 RPM
bodymap2_kidney 0 .00 RPM 3 .50 RPM
bodymap2_liver 0 .00 RPM 5 .36 RPM
bodymap2_lung 0 .00 RPM 0 .86 RPM
bodymap2_lymph_node 0 .00 RPM 0 .62 RPM
bodymap2_ovary 0 .00 RPM 3 .68 RPM
bodymap2_prostate 0 .00 RPM 2 .62 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .15 RPM
bodymap2_testis 0 .15 RPM 3 .70 RPM
bodymap2_thyroid 0 .00 RPM 10 .66 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .35 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3742 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3742 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3742 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3742 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3742 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 21 parental genes, and 175 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000089051 retrocopy
retro_acar_75,
Ailuropoda melanoleuca ENSAMEG000000139595 retrocopies
retro_amel_1362, retro_amel_1877, retro_amel_229, retro_amel_432, retro_amel_80,
Bos taurus ENSBTAG000000067958 retrocopies
retro_btau_1128, retro_btau_12, retro_btau_1483, retro_btau_1543, retro_btau_1628, retro_btau_246, retro_btau_265, retro_btau_94,
Canis familiaris ENSCAFG000000200145 retrocopies
retro_cfam_1249, retro_cfam_1543, retro_cfam_358, retro_cfam_618, retro_cfam_732,
Choloepus hoffmanni ENSCHOG0000000243437 retrocopies
retro_chof_1011, retro_chof_1019, retro_chof_1123, retro_chof_1213, retro_chof_1324, retro_chof_1410, retro_chof_1482, retro_chof_1550, retro_chof_163, retro_chof_1647, retro_chof_1659, retro_chof_1690, retro_chof_1705, retro_chof_1722, retro_chof_178, retro_chof_1781, retro_chof_1787, retro_chof_219, retro_chof_2264, retro_chof_2289, retro_chof_2319, retro_chof_2412, retro_chof_2466, retro_chof_2494, retro_chof_2632, retro_chof_2657, retro_chof_283, retro_chof_335, retro_chof_361, retro_chof_362, retro_chof_363, retro_chof_419, retro_chof_433, retro_chof_477, retro_chof_597, retro_chof_755, retro_chof_931,
Erinaceus europaeus ENSEEUG000000096532 retrocopies
retro_eeur_189, retro_eeur_231,
Felis catus ENSFCAG000000130388 retrocopies
retro_fcat_1007, retro_fcat_1112, retro_fcat_1294, retro_fcat_1435, retro_fcat_1627, retro_fcat_1920, retro_fcat_215, retro_fcat_354,
Homo sapiens ENSG00000140905 10 retrocopies
retro_hsap_1079, retro_hsap_1380, retro_hsap_2376, retro_hsap_275, retro_hsap_3308, retro_hsap_3389, retro_hsap_3742 , retro_hsap_3837, retro_hsap_4125, retro_hsap_465,
Gorilla gorilla ENSGGOG0000000023210 retrocopies
retro_ggor_1073, retro_ggor_1306, retro_ggor_1459, retro_ggor_1742, retro_ggor_1802, retro_ggor_2295, retro_ggor_2584, retro_ggor_2772, retro_ggor_320, retro_ggor_853,
Loxodonta africana ENSLAFG000000155863 retrocopies
retro_lafr_554, retro_lafr_822, retro_lafr_900,
Myotis lucifugus ENSMLUG0000000578312 retrocopies
retro_mluc_1151, retro_mluc_1221, retro_mluc_1466, retro_mluc_1538, retro_mluc_1659, retro_mluc_1685, retro_mluc_2089, retro_mluc_2090, retro_mluc_2139, retro_mluc_2314, retro_mluc_2411, retro_mluc_709,
Macaca mulatta ENSMMUG000000130885 retrocopies
retro_mmul_1192, retro_mmul_2202, retro_mmul_661, retro_mmul_840, retro_mmul_960,
Mustela putorius furoENSMPUG000000096774 retrocopies
retro_mputfur_1434, retro_mputfur_1492, retro_mputfur_349, retro_mputfur_809,
Nomascus leucogenys ENSNLEG000000268441 retrocopy
retro_nleu_365,
Procavia capensis ENSPCAG000000058201 retrocopy
retro_pcap_207,
Pongo abelii ENSPPYG0000000758515 retrocopies
retro_pabe_1146, retro_pabe_1147, retro_pabe_2146, retro_pabe_2728, retro_pabe_2785, retro_pabe_3060, retro_pabe_3121, retro_pabe_3288, retro_pabe_3289, retro_pabe_3479, retro_pabe_392, retro_pabe_393, retro_pabe_675, retro_pabe_676, retro_pabe_899,
Pan troglodytes ENSPTRG0000000838610 retrocopies
retro_ptro_1738, retro_ptro_2163, retro_ptro_230, retro_ptro_2304, retro_ptro_2381, retro_ptro_2540, retro_ptro_2613, retro_ptro_2802, retro_ptro_2803, retro_ptro_734,
Sarcophilus harrisii ENSSHAG000000055291 retrocopy
retro_shar_239,
Ictidomys tridecemlineatus ENSSTOG000000164332 retrocopies
retro_itri_31, retro_itri_34,
Tupaia belangeri ENSTBEG0000000005627 retrocopies
retro_tbel_1426, retro_tbel_1716, retro_tbel_1766, retro_tbel_1846, retro_tbel_1923, retro_tbel_2026, retro_tbel_2074, retro_tbel_2168, retro_tbel_2315, retro_tbel_2426, retro_tbel_2489, retro_tbel_2515, retro_tbel_2573, retro_tbel_2769, retro_tbel_3007, retro_tbel_3025, retro_tbel_311, retro_tbel_3140, retro_tbel_3458, retro_tbel_3852, retro_tbel_3924, retro_tbel_4173, retro_tbel_4727, retro_tbel_597, retro_tbel_601, retro_tbel_609, retro_tbel_825,
Tursiops truncatus ENSTTRG000000079928 retrocopies
retro_ttru_1052, retro_ttru_128, retro_ttru_1415, retro_ttru_1458, retro_ttru_1778, retro_ttru_211, retro_ttru_310, retro_ttru_795,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.05 RPM Legend:


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 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 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 .03 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

Indel association:

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





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