RetrogeneDB ID:

retro_hsap_4130

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:10532156..10532410(+)
Located in intron of:ENSG00000153707
Retrocopy
information
Ensembl ID:ENSG00000234360
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS12
Ensembl ID:ENSG00000112306
Aliases:None
Description:ribosomal protein S12 [Source:HGNC Symbol;Acc:10385]


Retrocopy-Parental alignment summary:






>retro_hsap_4130
CACCTTTATGTGTTTGCATCCAACTATGATAAATTTATGTATGTCACGACAGTGGGGACGCTGTGAGCTGAACAGCAAAT
CACTCTAATTAAGGTTGATGACAAGAACAAACTGAGGAAACTGGTAGGCCTCTGTAAAATTGACAGAGAGGGACAACCTC
ATAAACTGGTTGGTTGTAGTCATGTAGTAGTTAAGCAGTATGGCAAAGAATCTCAGGCCAAGAAAGTCACTGAAAATATT
TCAAATACAAAAAA

ORF - retro_hsap_4130 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.6 %
Parental protein coverage: 64.39 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalHLCVLASNCDEPMYVKLVEALCAEHQINLIKVDDNKKLGEWVGLCKIDREGKPRKVVGCSCVVVKDYGKE
HL.V.ASN.D..MYV..V..L.AE.QI.LIKVDD..KL...VGLCKIDREG.P.K.VGCS.VVVK.YGKE
RetrocopyHLYVFASNYDKFMYVTTVGTL*AEQQITLIKVDDKNKLRKLVGLCKIDREGQPHKLVGCSHVVVKQYGKE
ParentalSQAKDVIE-EYFKCKK
SQAK.V.E..YFK.KK
RetrocopySQAKKVTE<KYFKYKK

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 474 .15 RPM
bodymap2_adrenal 0 .00 RPM 588 .01 RPM
bodymap2_brain 0 .00 RPM 195 .61 RPM
bodymap2_breast 0 .00 RPM 380 .28 RPM
bodymap2_colon 0 .00 RPM 575 .74 RPM
bodymap2_heart 0 .00 RPM 153 .01 RPM
bodymap2_kidney 0 .00 RPM 295 .86 RPM
bodymap2_liver 0 .00 RPM 264 .93 RPM
bodymap2_lung 0 .00 RPM 735 .85 RPM
bodymap2_lymph_node 0 .00 RPM 1024 .27 RPM
bodymap2_ovary 0 .00 RPM 823 .31 RPM
bodymap2_prostate 0 .00 RPM 838 .38 RPM
bodymap2_skeletal_muscle 0 .00 RPM 323 .85 RPM
bodymap2_testis 0 .00 RPM 481 .66 RPM
bodymap2_thyroid 0 .00 RPM 378 .38 RPM
bodymap2_white_blood_cells 0 .00 RPM 1280 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4130 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4130 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4130 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4130 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4130 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_3473
Parental genes homology:
Parental genes homology involve 24 parental genes, and 192 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000104791 retrocopy
retro_acar_102,
Ailuropoda melanoleuca ENSAMEG000000080152 retrocopies
retro_amel_79, retro_amel_92,
Bos taurus ENSBTAG000000013607 retrocopies
retro_btau_106, retro_btau_1097, retro_btau_1306, retro_btau_1495, retro_btau_1514, retro_btau_1630, retro_btau_1802,
Callithrix jacchus ENSCJAG0000000286534 retrocopies
retro_cjac_1038, retro_cjac_1044, retro_cjac_1205, retro_cjac_1291, retro_cjac_1528, retro_cjac_1602, retro_cjac_1778, retro_cjac_1994, retro_cjac_2039, retro_cjac_2058, retro_cjac_2065, retro_cjac_2101, retro_cjac_2112, retro_cjac_2155, retro_cjac_2337, retro_cjac_2406, retro_cjac_2421, retro_cjac_2461, retro_cjac_2681, retro_cjac_2694, retro_cjac_2858, retro_cjac_301, retro_cjac_3310, retro_cjac_4149, retro_cjac_427, retro_cjac_466, retro_cjac_494, retro_cjac_592, retro_cjac_773, retro_cjac_805, retro_cjac_806, retro_cjac_807, retro_cjac_836, retro_cjac_977,
Cavia porcellus ENSCPOG000000004294 retrocopies
retro_cpor_1096, retro_cpor_304, retro_cpor_32, retro_cpor_380,
Equus caballus ENSECAG000000015998 retrocopies
retro_ecab_1012, retro_ecab_1131, retro_ecab_133, retro_ecab_744, retro_ecab_80, retro_ecab_828, retro_ecab_875, retro_ecab_959,
Echinops telfairi ENSETEG0000000685414 retrocopies
retro_etel_1129, retro_etel_1512, retro_etel_1580, retro_etel_2016, retro_etel_205, retro_etel_2082, retro_etel_2099, retro_etel_2169, retro_etel_26, retro_etel_280, retro_etel_29, retro_etel_55, retro_etel_578, retro_etel_915,
Felis catus ENSFCAG000000284027 retrocopies
retro_fcat_1084, retro_fcat_1314, retro_fcat_1446, retro_fcat_1880, retro_fcat_537, retro_fcat_664, retro_fcat_796,
Homo sapiens ENSG00000112306 26 retrocopies
retro_hsap_1241, retro_hsap_1522, retro_hsap_1738, retro_hsap_1771, retro_hsap_1797, retro_hsap_1962, retro_hsap_1992, retro_hsap_2249, retro_hsap_2264, retro_hsap_2667, retro_hsap_2722, retro_hsap_3043, retro_hsap_3079, retro_hsap_3249, retro_hsap_3347, retro_hsap_3428, retro_hsap_3467, retro_hsap_3640, retro_hsap_3680, retro_hsap_3994, retro_hsap_4130 , retro_hsap_599, retro_hsap_661, retro_hsap_702, retro_hsap_824, retro_hsap_895,
Gorilla gorilla ENSGGOG0000001223422 retrocopies
retro_ggor_1164, retro_ggor_1287, retro_ggor_1322, retro_ggor_139, retro_ggor_1426, retro_ggor_1441, retro_ggor_1686, retro_ggor_1861, retro_ggor_1894, retro_ggor_2115, retro_ggor_2241, retro_ggor_2261, retro_ggor_2339, retro_ggor_2456, retro_ggor_2489,