RetrogeneDB ID:

retro_hsap_60

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:90892075..90892429(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000238244
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:GABARAPL1
Ensembl ID:ENSG00000139112
Aliases:GABARAPL1, APG8-LIKE, APG8L, ATG8, ATG8B, ATG8L, GEC1
Description:GABA(A) receptor-associated protein like 1 [Source:HGNC Symbol;Acc:4068]


Retrocopy-Parental alignment summary:






>retro_hsap_60
ATGAAGTTCCAGTACAAGGAGGTCCATCCCTTTGAGTATCGGAAAAAGGAAGGAGAAAAGATCCGGAAGAAATATCCGGA
CAGGGTCCCCTTGATTGTAGAGAAGGCTCCAAAAGCAAGGGTGCCTGATCTGGACAGGAGGAAGTACCTAGTGCCCTCCG
ACCTTACCGATGGCCAGTTCTACCTTTTAATCCGGAAGAGAATCCACCTGAGACCTGAGGACGCCTTATTCTTCTTTGTC
AACAACACTATCCCTCCCACTAGTGCTACCATGGGCCAACTATATGAGGACAGTCATGAGGAAGATGATTTTCTGTATGT
GGCCTACAGTAATGAGAGTGTCTATGGGAAATGA

ORF - retro_hsap_60 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.16 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHL
MKFQYKE.HPFEYRKKEGEKIRKKYPDRVP.IVEKAPKARVPDLD.RKYLVPSDLT.GQFY.LIRKRIHL
RetrocopyMKFQYKEVHPFEYRKKEGEKIRKKYPDRVPLIVEKAPKARVPDLDRRKYLVPSDLTDGQFYLLIRKRIHL
ParentalRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK
RPEDALFFFVNNTIPPTSATMGQLYED.HEED.FLYVAYS.ESVYGK
RetrocopyRPEDALFFFVNNTIPPTSATMGQLYEDSHEEDDFLYVAYSNESVYGK

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 321 .47 RPM
bodymap2_adrenal 0 .00 RPM 50 .15 RPM
bodymap2_brain 0 .00 RPM 407 .60 RPM
bodymap2_breast 0 .00 RPM 138 .91 RPM
bodymap2_colon 0 .00 RPM 183 .23 RPM
bodymap2_heart 0 .00 RPM 267 .56 RPM
bodymap2_kidney 0 .00 RPM 480 .04 RPM
bodymap2_liver 0 .00 RPM 63 .24 RPM
bodymap2_lung 0 .00 RPM 355 .64 RPM
bodymap2_lymph_node 0 .00 RPM 111 .60 RPM
bodymap2_ovary 0 .00 RPM 64 .19 RPM
bodymap2_prostate 0 .00 RPM 170 .19 RPM
bodymap2_skeletal_muscle 0 .00 RPM 227 .93 RPM
bodymap2_testis 0 .00 RPM 68 .42 RPM
bodymap2_thyroid 0 .08 RPM 217 .31 RPM
bodymap2_white_blood_cells 0 .00 RPM 40 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_60 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_60 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_60 retrocopy 5' end.

Lab - click to see more details

retro_hsap_60 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_60 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_60
Parental genes homology:
Parental genes homology involve 11 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000067181 retrocopy
retro_cpor_232,
Equus caballus ENSECAG000000148321 retrocopy
retro_ecab_673,
Homo sapiens ENSG000000347131 retrocopy
retro_hsap_4115,
Homo sapiens ENSG00000139112 1 retrocopy
retro_hsap_60 ,
Homo sapiens ENSG000001409413 retrocopies
retro_hsap_3695, retro_hsap_487, retro_hsap_62,
Gorilla gorilla ENSGGOG000000223601 retrocopy
retro_ggor_1219,
Macropus eugenii ENSMEUG000000028733 retrocopies
retro_meug_1584, retro_meug_1840, retro_meug_905,
Oryctolagus cuniculus ENSOCUG000000168343 retrocopies
retro_ocun_1380, retro_ocun_496, retro_ocun_697,
Sarcophilus harrisii ENSSHAG000000074341 retrocopy
retro_shar_82,
Ictidomys tridecemlineatus ENSSTOG000000022461 retrocopy
retro_itri_391,
Tarsius syrichta ENSTSYG0000000530719 retrocopies
retro_tsyr_1045, retro_tsyr_1070, retro_tsyr_1101, retro_tsyr_1137, retro_tsyr_1308, retro_tsyr_1413, retro_tsyr_1467, retro_tsyr_1481, retro_tsyr_1671, retro_tsyr_1765, retro_tsyr_1800, retro_tsyr_234, retro_tsyr_573, retro_tsyr_761, retro_tsyr_796, retro_tsyr_832, retro_tsyr_864, retro_tsyr_978, retro_tsyr_999,

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 = 0.03 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 .00 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 .00 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 .00 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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