>retro_hsap_873
ATGGCGACGGGCGGCCAGCAGAAGGAGAACACGCTGCTTCACCTCTTCGCCGGCGGGTGTGGAGGCACAGTTGGTGCTAT
TTTCACTTGTCCACTAGAAGTCATTAAGACACGGTTGCAGTCTTTAAGATTAGCTCTCCGGACAGTCTACTATCCTCAGG
TTCATCTGGGGACCATTAGTGGAGCTGGAATGGTGAGACCAACATCCGTGACACCTGGACTCTTTCAGGTTCTGAAGTCG
ATCTTGGAGAAAGAGGGACCAAAGTCACTTTTTAGAGGCTTGGGTCCAAATTTGGTTGGAGTTGCACCATCAAGGGCTGT
ATACTTTGCATGTTACTCCAAAGCCAAAGAGCAATTTAATGGCATTTTCGTGCCTAACAGCAATATTGTGCATATTTTCT
CAGCTGGCTCTGCAGCTTTTATCACAAATTCCTTAATGAATCCTATATGGATGGTTAAAACCCGAATGCAGCTAGAACAG
AAAGTGAGGGGCTTTAAGCAGGTGAATACACTCCAGTGTGCTCGTTACGTTTACCAGACCGAAGGCATTCGTGGCTTCTA
TAGAGGATTAACTGCCTCGTATGCTGGAATTTCCGAAACTATAATCTGCTTTGCTATTTATGAAAGTTTAAAGAAGTATC
TGAAAGAAGCTCCATTAGCCTCTTCTGCAAATGGGACTGAGAAAAATTCCACAAGTTTTTTTGGACTTATGGCAGCTGCT
GCTCTTTCTAAGGGCTGTGCCTCCTGCATTGCTTATCCACACGAAGTTATAAGGACGAGGCTCCGGGAAGAGGGCACCAA
GTACAAGTCTTTTGTCCAGACGGCGCGCCTGGTGTTCCAGGAAGAAGGCTACCTCGCCTTTTATAGAGGACTGTTTGCCC
AGCTTATCCGGCGGATCCCAAATACTGCCATTGTGTTGTCTACTTATGAGTTAATTGTGTACCTGTTAGAAGACCGTACT
CAG
ORF - retro_hsap_873 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: |
98.44 % |
Parental protein coverage: |
100. % |
Number of stop codons detected: |
0 |
Number of frameshifts detected |
0 |
Retrocopy - Parental Gene Alignment:
Parental | MATGGQQKENTLLHLFAGGCGGTVGAIFTCPLEVIKTRLQSSRLALRTVYYPQVHLGTISGAGMVRPTSV |
| MATGGQQKENTLLHLFAGGCGGTVGAIFTCPLEVIKTRLQS.RLALRTVYYPQVHLGTISGAGMVRPTSV |
Retrocopy | MATGGQQKENTLLHLFAGGCGGTVGAIFTCPLEVIKTRLQSLRLALRTVYYPQVHLGTISGAGMVRPTSV |
|
Parental | TPGLFQVLKSILEKEGPKSLFRGLGPNLVGVAPSRAVYFACYSKAKEQFNGIFVPNSNIVHIFSAGSAAF |
| TPGLFQVLKSILEKEGPKSLFRGLGPNLVGVAPSRAVYFACYSKAKEQFNGIFVPNSNIVHIFSAGSAAF |
Retrocopy | TPGLFQVLKSILEKEGPKSLFRGLGPNLVGVAPSRAVYFACYSKAKEQFNGIFVPNSNIVHIFSAGSAAF |
|
Parental | ITNSLMNPIWMVKTRMQLEQKVRGSKQMNTLQCARYVYQTEGIRGFYRGLTASYAGISETIICFAIYESL |
| ITNSLMNPIWMVKTRMQLEQKVRG.KQ.NTLQCARYVYQTEGIRGFYRGLTASYAGISETIICFAIYESL |
Retrocopy | ITNSLMNPIWMVKTRMQLEQKVRGFKQVNTLQCARYVYQTEGIRGFYRGLTASYAGISETIICFAIYESL |
|
Parental | KKYLKEAPLASSANGTEKNSTSFFGLMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLVFR |
| KKYLKEAPLASSANGTEKNSTSFFGLMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLVF. |
Retrocopy | KKYLKEAPLASSANGTEKNSTSFFGLMAAAALSKGCASCIAYPHEVIRTRLREEGTKYKSFVQTARLVFQ |
|
Parental | EEGYLAFYRGLFAQLIRQIPNTAIVLSTYELIVYLLEDRTQ |
| EEGYLAFYRGLFAQLIR.IPNTAIVLSTYELIVYLLEDRTQ |
Retrocopy | EEGYLAFYRGLFAQLIRRIPNTAIVLSTYELIVYLLEDRTQ |
|
Legend:
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
(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 .06 RPM |
7 .26 RPM |
bodymap2_adrenal |
0 .43 RPM |
5 .26 RPM |
bodymap2_brain |
0 .98 RPM |
20 .16 RPM |
bodymap2_breast |
0 .51 RPM |
35 .21 RPM |
bodymap2_colon |
0 .10 RPM |
6 .28 RPM |
bodymap2_heart |
0 .00 RPM |
11 .32 RPM |
bodymap2_kidney |
0 .68 RPM |
21 .45 RPM |
bodymap2_liver |
0 .32 RPM |
27 .92 RPM |
bodymap2_lung |
0 .05 RPM |
4 .15 RPM |
bodymap2_lymph_node |
0 .02 RPM |
5 .19 RPM |
bodymap2_ovary |
0 .19 RPM |
7 .33 RPM |
bodymap2_prostate |
0 .38 RPM |
8 .16 RPM |
bodymap2_skeletal_muscle |
0 .15 RPM |
22 .73 RPM |
bodymap2_testis |
11 .44 RPM |
27 .51 RPM |
bodymap2_thyroid |
0 .06 RPM |
11 .86 RPM |
bodymap2_white_blood_cells |
0 .02 RPM |
5 .79 RPM |
RNA Polymerase II actvity near the 5' end of retro_hsap_873 was not detected
13 EST(s) were mapped to retro_hsap_873 retrocopy
EST ID |
Start |
End |
Identity |
Match |
Mis-match |
Score |
AA352224 |
49455579 |
49455766 |
100 |
187 |
0 |
187 |
AA398466 |
49454974 |
49455380 |
99.6 |
404 |
2 |
402 |
AA401872 |
49455019 |
49455393 |
99.8 |
372 |
1 |
370 |
AA757281 |
49454976 |
49455435 |
99.8 |
458 |
1 |
457 |
AA844723 |
49454973 |
49455385 |
100 |
412 |
0 |
412 |
AI200893 |
49454963 |
49455467 |
100 |
499 |
0 |
498 |
AI201028 |
49454967 |
49455426 |
99.8 |
458 |
1 |
457 |
AI201164 |
49454963 |
49455463 |
99 |
500 |
0 |
498 |
AW235374 |
49454976 |
49455337 |
97.8 |
360 |
1 |
356 |
BF059403 |
49454976 |
49455337 |
100 |
361 |
0 |
361 |
HY199799 |
49454979 |
49455441 |
99.8 |
460 |
1 |
458 |
HY212112 |
49454979 |
49455426 |
100 |
447 |
0 |
447 |
HY239480 |
49454979 |
49455409 |
100 |
430 |
0 |
430 |
No TSS is located nearby retro_hsap_873 retrocopy 5' end.
retro_hsap_873 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_hsap_873 has 0 orthologous retrocopies within eutheria group .
Parental genes homology:
Parental genes homology involve
6 parental genes, and
6 retrocopies.
Expression level across human populations :
Library |
Retrogene expression |
CEU_NA11831 |
0 .06 RPM |
CEU_NA11843 |
0 .03 RPM |
CEU_NA11930 |
0 .13 RPM |
CEU_NA12004 |
0 .08 RPM |
CEU_NA12400 |
0 .11 RPM |
CEU_NA12751 |
0 .02 RPM |
CEU_NA12760 |
0 .13 RPM |
CEU_NA12827 |
0 .09 RPM |
CEU_NA12872 |
0 .14 RPM |
CEU_NA12873 |
0 .13 RPM |
FIN_HG00183 |
0 .08 RPM |
FIN_HG00277 |
0 .15 RPM |
FIN_HG00315 |
0 .03 RPM |
FIN_HG00321 |
0 .09 RPM |
FIN_HG00328 |
0 .09 RPM |
FIN_HG00338 |
0 .02 RPM |
FIN_HG00349 |
0 .17 RPM |
FIN_HG00375 |
0 .07 RPM |
FIN_HG00377 |
0 .13 RPM |
FIN_HG00378 |
0 .08 RPM |
GBR_HG00099 |
0 .09 RPM |
GBR_HG00111 |
0 .04 RPM |
GBR_HG00114 |
0 .03 RPM |
GBR_HG00119 |
0 .02 RPM |
GBR_HG00131 |
0 .03 RPM |
GBR_HG00133 |
0 .12 RPM |
GBR_HG00134 |
0 .07 RPM |
GBR_HG00137 |
0 .16 RPM |
GBR_HG00142 |
0 .06 RPM |
GBR_HG00143 |
0 .10 RPM |
TSI_NA20512 |
0 .06 RPM |
TSI_NA20513 |
0 .07 RPM |
TSI_NA20518 |
0 .25 RPM |
TSI_NA20532 |
0 .10 RPM |
TSI_NA20538 |
0 .23 RPM |
TSI_NA20756 |
0 .12 RPM |
TSI_NA20765 |
0 .04 RPM |
TSI_NA20771 |
0 .11 RPM |
TSI_NA20786 |
0 .05 RPM |
TSI_NA20798 |
0 .06 RPM |
YRI_NA18870 |
0 .14 RPM |
YRI_NA18907 |
0 .07 RPM |
YRI_NA18916 |
0 .00 RPM |
YRI_NA19093 |
0 .03 RPM |
YRI_NA19099 |
0 .32 RPM |
YRI_NA19114 |
0 .05 RPM |
YRI_NA19118 |
0 .10 RPM |
YRI_NA19213 |
0 .05 RPM |
YRI_NA19214 |
0 .10 RPM |
YRI_NA19223 |
0 .06 RPM |
Indel association:
No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (
PubMed).