RetrogeneDB ID:

retro_hsap_1207

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:57888874..57889602(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000234421
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC25A6
Ensembl ID:ENSG00000169100
Aliases:None
Description:solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6 [Source:HGNC Symbol;Acc:10992]


Retrocopy-Parental alignment summary:






>retro_hsap_1207
ATGACAGATGATGCTGTGTCCTTCAACAGGGACTTCTGGCAGGTGGGGTGGTCACAGCCATCTCTAAGGCAGCAGGAGCA
CCTATCGAGTGGCTCAAGCTGCTGCTGCAGGTGCAGCATGCCACCAAGGAAATTACCACAGATAAGCAGTACAAGCACAT
TATAGACTGTGTGGTCTGTATTCCCAAGGAGGAGAGAGTCCTGTCCTTCTGGCGTGGTAACCTGGCCAATGTCATCAGAT
ATTTCCCCACCCAGGGGCTCTCAACTTCGCCTTCGAAATAAGTACTAGCAGATCTTCCTGGGTAGTGTGGACAAGAGGAC
CCACTTTCAGCACTATGTTGCAAGGAACCTGGCATCAGGCGTGCGCTGGGGCCACATCCTTGTGTTTTGTGTACCCTCTT
GATTTTGTCTGTACCAATCTACCAGTGGATGTGGGTAAAGCTGGAGCTAAAAGGGAATTCAGAAGCCTTGGTGACTGTCT
GGTTAAGATCTACAAATCTAATAGGATTAAGGGCCTGCACCAAGGCTTTACCATGTCTGTGCAGGGTATTAGCATCTACC
CAGCTGCCTACTTCAGTATCTGTGACACTGCAAAGGGAATGCTTCCAGATTCCAAGAGTACTACATCATCATCAGCTGAA
TGATTACACACAGCCTGTCATTGTCATTGCAGGGTTGAATTCCTATCCATTTGACACTGTTCACTGCTAAATGTCGATGC
AGTCAGGC

ORF - retro_hsap_1207 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.86 %
Parental protein coverage: 81.54 %
Number of stop codons detected: 2
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMTEQAISFAKDF-LAGGIAAAISKTAVAPIERVKLLLQVQHASKQIAADKQYKGIVDCIVRIPKEQGVLS
MT..A.SF..DF.LAGG...AISK.A.APIE..KLLLQVQHA.K.I..DKQYK.I.DC.V.IPKE..VLS
RetrocopyMTDDAVSFNRDF<LAGGVVTAISKAAGAPIEWLKLLLQVQHATKEITTDKQYKHIIDCVVCIPKEERVLS
ParentalFWRGNLANVIRY-FPTQ-ALNFAF-KDKYKQIFLGGVDKHTQFWRYFAGNLASGGA-AGATSLCFVYPLD
FWRGNLANVIRY.FP...ALNFAF...KY.QIFLG.VDK.T.F...........G..AGATSLCFVYPLD
RetrocopyFWRGNLANVIRY<FPHPGALNFAF<RNKY*QIFLGSVDKRTHF-QHYVARNLASGV>AGATSLCFVYPLD
ParentalFARTRLAADVGKSGTEREFRGLGDCLVKITKSDGIRGLYQGFSVSVQGIIIYRAAYFGVYDTAKGMLPD-
F..T.L..DVGK.G..REFR.LGDCLVKI.KS..I.GL.QGF..SVQGI.IY.AAYF...DTAKGMLPD.
RetrocopyFVCTNLPVDVGKAGAKREFRSLGDCLVKIYKSNRIKGLHQGFTMSVQGISIYPAAYFSICDTAKGMLPD>
ParentalPKNTHIVVSWMIAQTVTAVAGVVSYPFDTVRRRMMMQSG
P...H........Q.V...AG..SYPFDTV...M.MQSG
RetrocopyPRVLHHHQLNDYTQPVIVIAGLNSYPFDTVHC*MSMQSG

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 314 .07 RPM
bodymap2_adrenal 0 .00 RPM 338 .52 RPM
bodymap2_brain 0 .00 RPM 77 .31 RPM
bodymap2_breast 0 .00 RPM 243 .60 RPM
bodymap2_colon 0 .00 RPM 328 .05 RPM
bodymap2_heart 0 .00 RPM 54 .59 RPM
bodymap2_kidney 0 .00 RPM 175 .14 RPM
bodymap2_liver 0 .00 RPM 42 .12 RPM
bodymap2_lung 0 .00 RPM 179 .15 RPM
bodymap2_lymph_node 0 .00 RPM 193 .70 RPM
bodymap2_ovary 0 .00 RPM 334 .67 RPM
bodymap2_prostate 0 .00 RPM 261 .14 RPM
bodymap2_skeletal_muscle 0 .00 RPM 72 .51 RPM
bodymap2_testis 0 .00 RPM 138 .91 RPM
bodymap2_thyroid 0 .00 RPM 240 .40 RPM
bodymap2_white_blood_cells 0 .00 RPM 294 .37 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1207 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1207 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1207 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1207 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1207 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_941
Pongo abelii retro_pabe_1006
Parental genes homology:
Parental genes homology involve 9 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000056091 retrocopy
retro_amel_255,
Homo sapiens ENSG000000050227 retrocopies
retro_hsap_2243, retro_hsap_3132, retro_hsap_3336, retro_hsap_3516, retro_hsap_3715, retro_hsap_3730, retro_hsap_4239,
Homo sapiens ENSG00000169100 5 retrocopies
retro_hsap_1207 , retro_hsap_150, retro_hsap_2460, retro_hsap_4147, retro_hsap_4207,
Gorilla gorilla ENSGGOG000000230042 retrocopies
retro_ggor_239, retro_ggor_2785,
Loxodonta africana ENSLAFG000000015841 retrocopy
retro_lafr_713,
Microcebus murinus ENSMICG000000061362 retrocopies
retro_mmur_1021, retro_mmur_922,
Macaca mulatta ENSMMUG000000068991 retrocopy
retro_mmul_1182,
Nomascus leucogenys ENSNLEG000000003891 retrocopy
retro_nleu_895,
Otolemur garnettii ENSOGAG000000009632 retrocopies
retro_ogar_2492, retro_ogar_2499,

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 ) 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 .00 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:

The presence of retro_hsap_1207 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1207 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 13:57865912..57892000 95.08 94.32 90.72 99.24 100 100 100 100 100 100 99.49 100 100 100

Indel #1, located at the genomic coordinates 13:57865912..57892000.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 99.24 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 95.08 % Yoruba in Ibadan,Nigeria YRI 94.32 % Luhya in Webuye,Kenya LWK 90.72 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 99.49 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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