RetrogeneDB ID:

retro_hsap_1347

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:60625731..60626044(+)
Located in intron of:ENSG00000126773
Retrocopy
information
Ensembl ID:ENSG00000258896
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SCOC
Ensembl ID:ENSG00000153130
Aliases:SCOC, SCOCO
Description:short coiled-coil protein [Source:HGNC Symbol;Acc:20335]


Retrocopy-Parental alignment summary:






>retro_hsap_1347
CTCTCCCAGCACCTCAAACATTCATCAAGGATTTTGTATCCAAGGCCCAAAAGTTTGTTACCCAAGACGACAAATATTGA
CATGGATGCAGTTGATGCTGAAAATCATTTGGAATTGGAGGGAAAAACACAGCTTATTAATCAAGTGTTGGAACCCCAAC
ATACACTTCAAGATCTCCCTGTCAGAGGAGATGCGGTTACGGAAGAAAATCTCAAGCTAAAATCAGAAAACCAAGTTTCT
TAGACAATACACAGAAAATTTCATGTCAGCTTCTAGTGTTTTTCAAACAACTGACACAAAAAGCAAAAGAAAA

ORF - retro_hsap_1347 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.05 %
Parental protein coverage: 85.25 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalLADDIDHSSRILYPRPKSLLPKMMNADMDAVDAENQVELEEKTRLINQVLELQHTLEDLSARVDAVKEEN
L.....HSSRILYPRPKSLLPK..N.DMDAVDAEN..ELE.KT.LINQVLE.QHTL.DL..R.DAV.EEN
RetrocopyLSQHLKHSSRILYPRPKSLLPKTTNIDMDAVDAENHLELEGKTQLINQVLEPQHTLQDLPVRGDAVTEEN
ParentalLKLKSENQV-LGQYIENLMSASSVFQTTDTKSKRK
LKLKSENQV.L.QY.EN.MSASSVFQTTDTKSKRK
RetrocopyLKLKSENQV>LRQYTENFMSASSVFQTTDTKSKRK

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 .00 RPM 37 .11 RPM
bodymap2_adrenal 0 .18 RPM 47 .04 RPM
bodymap2_brain 0 .00 RPM 218 .32 RPM
bodymap2_breast 0 .00 RPM 73 .31 RPM
bodymap2_colon 0 .00 RPM 73 .19 RPM
bodymap2_heart 0 .13 RPM 81 .56 RPM
bodymap2_kidney 0 .12 RPM 142 .72 RPM
bodymap2_liver 0 .00 RPM 50 .87 RPM
bodymap2_lung 0 .04 RPM 62 .76 RPM
bodymap2_lymph_node 0 .00 RPM 41 .99 RPM
bodymap2_ovary 0 .33 RPM 71 .36 RPM
bodymap2_prostate 0 .00 RPM 85 .01 RPM
bodymap2_skeletal_muscle 0 .00 RPM 25 .52 RPM
bodymap2_testis 0 .02 RPM 80 .88 RPM
bodymap2_thyroid 0 .04 RPM 76 .81 RPM
bodymap2_white_blood_cells 0 .00 RPM 35 .63 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1347 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1347 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1347 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1347 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1347 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_922
Gorilla gorilla retro_ggor_1048
Pongo abelii retro_pabe_1119
Macaca mulatta retro_mmul_2186
Callithrix jacchus retro_cjac_713
Parental genes homology:
Parental genes homology involve 23 parental genes, and 62 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000109572 retrocopies
retro_amel_176, retro_amel_725,
Bos taurus ENSBTAG000000221092 retrocopies
retro_btau_1843, retro_btau_1847,
Canis familiaris ENSCAFG000000036992 retrocopies
retro_cfam_1564, retro_cfam_667,
Choloepus hoffmanni ENSCHOG0000000060410 retrocopies
retro_chof_1154, retro_chof_1651, retro_chof_1973, retro_chof_1980, retro_chof_2214, retro_chof_2394, retro_chof_2595, retro_chof_289, retro_chof_563, retro_chof_862,
Callithrix jacchus ENSCJAG000000030602 retrocopies
retro_cjac_713, retro_cjac_95,
Dipodomys ordii ENSDORG000000001778 retrocopies
retro_dord_359, retro_dord_461, retro_dord_476, retro_dord_578, retro_dord_634, retro_dord_639, retro_dord_712, retro_dord_724,
Erinaceus europaeus ENSEEUG000000111071 retrocopy
retro_eeur_19,
Homo sapiens ENSG00000153130 2 retrocopies
retro_hsap_1347 , retro_hsap_228,
Gorilla gorilla ENSGGOG000000281862 retrocopies
retro_ggor_1048, retro_ggor_291,
Macropus eugenii ENSMEUG000000145342 retrocopies
retro_meug_1580, retro_meug_823,
Macaca mulatta ENSMMUG000000223511 retrocopy
retro_mmul_2186,
Monodelphis domestica ENSMODG000000255282 retrocopies
retro_mdom_1163, retro_mdom_1265,
Mustela putorius furoENSMPUG000000161192 retrocopies
retro_mputfur_468, retro_mputfur_708,
Nomascus leucogenys ENSNLEG000000050812 retrocopies
retro_nleu_1830, retro_nleu_849,
Oryctolagus cuniculus ENSOCUG000000065913 retrocopies
retro_ocun_1400, retro_ocun_1657, retro_ocun_429,
Otolemur garnettii ENSOGAG000000264142 retrocopies
retro_ogar_2489, retro_ogar_3043,
Procavia capensis ENSPCAG000000031652 retrocopies
retro_pcap_119, retro_pcap_457,
Pongo abelii ENSPPYG000000150772 retrocopies
retro_pabe_1119, retro_pabe_423,
Pan troglodytes ENSPTRG000000164602 retrocopies
retro_ptro_198, retro_ptro_922,
Sarcophilus harrisii ENSSHAG000000034741 retrocopy
retro_shar_572,
Ictidomys tridecemlineatus ENSSTOG000000285293 retrocopies
retro_itri_1170, retro_itri_357, retro_itri_451,
Tarsius syrichta ENSTSYG000000118146 retrocopies
retro_tsyr_1232, retro_tsyr_1446, retro_tsyr_1566, retro_tsyr_2025, retro_tsyr_34, retro_tsyr_446,
Tursiops truncatus ENSTTRG000000106771 retrocopy
retro_ttru_123,

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 = 0.18 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .10 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .04 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .12 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .12 RPM
GBR_HG00134 0 .13 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .18 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .15 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .15 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



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