RetrogeneDB ID: | retro_hsap_4862 | ||
Retrocopylocation | Organism: | Human (Homo sapiens) | |
Coordinates: | X:74963062..74966746(-) | ||
Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSG00000215105 | |
Aliases: | None | ||
Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
Parental gene symbol: | TTC3 | ||
Ensembl ID: | ENSG00000182670 | ||
Aliases: | TTC3, DCRR1, RNF105, TPRDIII | ||
Description: | tetratricopeptide repeat domain 3 [Source:HGNC Symbol;Acc:12393] |
Percent Identity: | 93.08 % |
Parental protein coverage: | 60.64 % |
Number of stop codons detected: | 0 |
Number of frameshifts detected | 0 |
Parental | DNFAEGDFTVADYALLEDCPHVDDCVFAAEFMSNDYVRVTQLYCDGVGVQYKDYIQSERNLEFDICSIWC |
DNFAEGDFT.ADYALLEDCP.VDDCVFAAEFM..DYVRVTQLYCDGVG.QYKDY.QSERNLEFDICSIWC | |
Retrocopy | DNFAEGDFTMADYALLEDCPYVDDCVFAAEFMTDDYVRVTQLYCDGVGKQYKDYVQSERNLEFDICSIWC |
Parental | SKPISVLQDYCDAIKINIFWPLLFQHQNSSVISRLHPCVDANNSRASEINLKKLQHLELMEDIVDLAKKV |
SKPISVLQDYCDAIKINIFWPLLFQHQNSSVISRLHPCVDANNSRASEINLK.LQHLELMEDIVDLAKK. | |
Retrocopy | SKPISVLQDYCDAIKINIFWPLLFQHQNSSVISRLHPCVDANNSRASEINLKRLQHLELMEDIVDLAKKA |
Parental | ANDSFLIGGLLRIGCKIENKILAMEEALNWIKYAGDVTILTKLGSIDNCWPMLSIFFTEYKYHITKIVME |
ANDS.LIGGLLRIG.KIENKILAMEEALNWIKYAGDVTILTKLGSIDNCWPMLSIFFTEYKYHITKIVME | |
Retrocopy | ANDSLLIGGLLRIGYKIENKILAMEEALNWIKYAGDVTILTKLGSIDNCWPMLSIFFTEYKYHITKIVME |
Parental | DCNLLEELKTQSCMDCIEEGELMKMKGNEEFSKERFDIAIIYYTRAIEYRPENYLLYGNRALCFLRTGQF |
DCNLLEELKTQSCMDCIE.GELMKMKGNEEFSKERFDIAIIYYTRAIEYRPEN.LLYGNRALCFLRTGQF | |
Retrocopy | DCNLLEELKTQSCMDCIEQGELMKMKGNEEFSKERFDIAIIYYTRAIEYRPENHLLYGNRALCFLRTGQF |
Parental | RNALGDGKRATILKNTWPKGHYRYCDALSMLGEYDWALQANIKAQKLCKNDPEGIKDLIQQHVKLQKQIE |
RNALGDGKRATILKNTWPKGHYRYCDALSMLGEY.WALQANI.AQKLCKNDPEGIKDLIQQHVKLQKQIE | |
Retrocopy | RNALGDGKRATILKNTWPKGHYRYCDALSMLGEYNWALQANITAQKLCKNDPEGIKDLIQQHVKLQKQIE |
Parental | DLQGRTANKDPIKAFYENRAYTPRSLSAPIFTTSLNFVEKERDFRKINHEMANGGNQNLKVADEALKVDD |
DLQGRTANK.PIKAFYENRAYTPRSLSAP.F.TSLNFVEKERDFRKINHEMANGGNQNLKV.DEAL.VDD | |
Retrocopy | DLQGRTANKNPIKAFYENRAYTPRSLSAPVFSTSLNFVEKERDFRKINHEMANGGNQNLKVMDEALMVDD |
Parental | CDCHPEFSPPSSQPPKHKGKQKSRNNESEKFSSSSPLTLPADLKNILEKQFSKSSRAAHQDFANIMKMLR |
CDCHPEFSPPSSQPPKHKGKQKSRNNESEKFSSSS.LTLPADLKNILEKQFSKSSR.AHQDFANIM.MLR | |
Retrocopy | CDCHPEFSPPSSQPPKHKGKQKSRNNESEKFSSSSQLTLPADLKNILEKQFSKSSRGAHQDFANIMTMLR |
Parental | SLIQDGYMALLEQRCRSAAQAFTELLNGLDPQKIKQLNLAMINYVLVVYGLAISLLGIGQPEELSEAENQ |
SLIQDGY.ALLEQRCRSAA.AFTELLNGLDPQKIKQLNLAMINYVLVVYGLAISLLGIGQPEELSEAENQ | |
Retrocopy | SLIQDGYTALLEQRCRSAAHAFTELLNGLDPQKIKQLNLAMINYVLVVYGLAISLLGIGQPEELSEAENQ |
Parental | FKRIIEHYPSEGLDCLAYCGIGKVYLKKNRFLEALNHFEKARTLIYRLPGVLTWPTSNVIIEESQPQKIK |
FKRIIEHY..EGLDCLAYCGIGKVYL...RFLEALNHFEKARTLIYRLPGVLTWPTSNVIIEESQP.KIK | |
Retrocopy | FKRIIEHYHNEGLDCLAYCGIGKVYLXXXRFLEALNHFEKARTLIYRLPGVLTWPTSNVIIEESQPEKIK |
Parental | MLLEKFVEECKFPPVPDAICCYQKCHGYSKIQIYITDPDFKGFIRISCCQYCKIEFHMNCWKKLKTTTFN |
MLLEKFVEECKFPPVPDAICCYQKC.GYSKIQIYITDPDFKGFIRISCCQYCKIEFHMNCWKKLKTTTFN | |
Retrocopy | MLLEKFVEECKFPPVPDAICCYQKCCGYSKIQIYITDPDFKGFIRISCCQYCKIEFHMNCWKKLKTTTFN |
Parental | DKIDKDFLQGICLTPDCEGVISKIIIFSSGGEVKCEFEHKVIKEKVPPRPILKQKCSSLEKLRLKEDKKL |
DKIDKDFLQGICLTPDCEGVISKIIIFSSGG.VKCEFEHKVIKEKVPPRPILKQKCSSLEKLRLKED... | |
Retrocopy | DKIDKDFLQGICLTPDCEGVISKIIIFSSGGQVKCEFEHKVIKEKVPPRPILKQKCSSLEKLRLKEDXXX |
Parental | KRKIQKKEAKKLAQERMEEDLRESNPPKNEEQKETVDNVQRCQFLDDRILQCIKQYADKIKSGIQNTAML |
...........LAQERMEEDLRESNPPKNEEQKETVDNVQ.CQFLDDRILQCIKQYADKIKSGI.NTA.L | |
Retrocopy | XXXXXXXXXXXLAQERMEEDLRESNPPKNEEQKETVDNVQHCQFLDDRILQCIKQYADKIKSGIWNTATL |
Parental | LKELLSWKVLSTEDYTTCFSSRNFLNEAVDYVIRHLIQENNRVKTRIFLHVLSELKEVEPKLAAWIQKLN |
LKELLSWKVLSTEDYTTCFSSRNFLNEAVDYVIRHLIQE.NRVKTRIFLHVLSELKEVEPKLAAWI.KLN | |
Retrocopy | LKELLSWKVLSTEDYTTCFSSRNFLNEAVDYVIRHLIQEKNRVKTRIFLHVLSELKEVEPKLAAWIRKLN |
Parental | SFGLDATGTFFSRYGASLKLLDFSIMTFLWNEKYGHKLDSIEGKQLDYFSEPASLKEARCLIWLLEEHRD |
SFGLDATG.FFSRY.ASLK.LDFSIMTFLWNEKYGHKLDSIEGKQLDYF.EP.S.KEARCLIWLLEEHRD | |
Retrocopy | SFGLDATGPFFSRYEASLKQLDFSIMTFLWNEKYGHKLDSIEGKQLDYFFEPTSSKEARCLIWLLEEHRD |
Parental | KFPALHSALDEFFDIMDSRCTVLRKQDSGEAPFSSTKVKNKSKKKKPKDSKPMLVGSGTTSVTSNNEIIT |
KFPALHSALDEFFDIMDSRCTVLRKQDSGEAPFSSTKVKNK.KKKKPKDSKPMLVGSGTTSVT.NNEIIT | |
Retrocopy | KFPALHSALDEFFDIMDSRCTVLRKQDSGEAPFSSTKVKNKGKKKKPKDSKPMLVGSGTTSVTPNNEIIT |
Parental | SSEDHSNRNSDSAGPFAVPDHLRQDVEEFEALYDQHSNEYVVRNKKLWDMNPKQKCSTLYDYFSQFLEEH |
SSEDHSN.NSD.AGPFAVPDHLRQDVEEFEALYDQHSNEYVVRNKKLWDMNPKQKCSTLYDYFSQ.LEEH | |
Retrocopy | SSEDHSNQNSDTAGPFAVPDHLRQDVEEFEALYDQHSNEYVVRNKKLWDMNPKQKCSTLYDYFSQLLEEH |
Parental | GPLDMSNKMFSAEYEFFPEETRQILEKAGGLKPFLLGCPRFVVIDNCIALKKVASRLKKKRKKKNIKTKV |
GPLDMS.KMFS.EYEFFPEETR.ILEKAGGLK.FLLGCPRFVVIDNCIALKKVASRL............. | |
Retrocopy | GPLDMSHKMFSEEYEFFPEETRPILEKAGGLKSFLLGCPRFVVIDNCIALKKVASRLXXXXXXXXXXXXX |
Parental | EEISKAGEYVRVKLQLNPAAREFKPDVKSKPVSDSSSA |
E.ISKAGEY..VKL.LN.AAREFKPDVKSKPVS.SSSA | |
Retrocopy | EDISKAGEYLQVKLPLNSAAREFKPDVKSKPVSGSSSA |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
Library | Retrocopy expression | Parental gene expression |
---|---|---|
bodymap2_adipose | 4 .61 RPM | 211 .78 RPM |
bodymap2_adrenal | 3 .21 RPM | 139 .29 RPM |
bodymap2_brain | 8 .79 RPM | 304 .25 RPM |
bodymap2_breast | 6 .75 RPM | 285 .63 RPM |
bodymap2_colon | 4 .76 RPM | 156 .27 RPM |
bodymap2_heart | 2 .92 RPM | 70 .37 RPM |
bodymap2_kidney | 3 .12 RPM | 126 .58 RPM |
bodymap2_liver | 0 .46 RPM | 96 .34 RPM |
bodymap2_lung | 2 .32 RPM | 98 .17 RPM |
bodymap2_lymph_node | 2 .19 RPM | 144 .00 RPM |
bodymap2_ovary | 10 .27 RPM | 292 .72 RPM |
bodymap2_prostate | 3 .78 RPM | 216 .24 RPM |
bodymap2_skeletal_muscle | 0 .38 RPM | 47 .09 RPM |
bodymap2_testis | 6 .88 RPM | 245 .15 RPM |
bodymap2_thyroid | 6 .55 RPM | 194 .43 RPM |
bodymap2_white_blood_cells | 0 .39 RPM | 140 .49 RPM |
EST ID | Start | End | Identity | Match | Mis-match | Score |
---|---|---|---|---|---|---|
AA470510 | 74963205 | 74963587 | 99.3 | 379 | 3 | 376 |
AA470557 | 74963367 | 74963779 | 99.8 | 410 | 1 | 408 |
AA502576 | 74963237 | 74963592 | 99.2 | 355 | 0 | 354 |
AA554904 | 74963213 | 74963693 | 98.8 | 474 | 5 | 467 |
AI678227 | 74963212 | 74963806 | 100 | 589 | 0 | 585 |
AU117751 | 74964281 | 74964986 | 99.2 | 695 | 6 | 689 |
AU127587 | 74964451 | 74965056 | 99.5 | 597 | 2 | 593 |
AU144640 | 74964410 | 74964956 | 99.5 | 539 | 3 | 534 |
BM701975 | 74963702 | 74964250 | 99.9 | 547 | 1 | 546 |
BU729641 | 74963205 | 74963862 | 99.9 | 653 | 1 | 651 |
BX495640 | 74963822 | 74964327 | 97.9 | 503 | 2 | 497 |
DA200641 | 74964721 | 74965296 | 100 | 575 | 0 | 575 |
DA494480 | 74964305 | 74964851 | 100 | 545 | 0 | 544 |
DA509421 | 74964256 | 74964836 | 100 | 580 | 0 | 580 |
DB355669 | 74963215 | 74963709 | 98.6 | 479 | 3 | 468 |
TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
---|---|---|---|---|---|---|
no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
TSS #1 | TSS_201219 | 866 libraries | 572 libraries | 358 libraries | 31 libraries | 2 libraries |
Species | RetrogeneDB ID |
---|---|
Gorilla gorilla | retro_ggor_3032 |
Species | Parental gene accession | Retrocopies number | |
---|---|---|---|
Homo sapiens | ENSG00000182670 | 2 retrocopies |
retro_hsap_4862 , retro_hsap_886,
|
Gorilla gorilla | ENSGGOG00000011116 | 1 retrocopy | |
Nomascus leucogenys | ENSNLEG00000004545 | 1 retrocopy |
Library | Retrogene expression |
---|---|
CEU_NA11831 | 0 .26 RPM |
CEU_NA11843 | 0 .09 RPM |
CEU_NA11930 | 0 .16 RPM |
CEU_NA12004 | 0 .23 RPM |
CEU_NA12400 | 0 .14 RPM |
CEU_NA12751 | 0 .61 RPM |
CEU_NA12760 | 0 .27 RPM |
CEU_NA12827 | 0 .09 RPM |
CEU_NA12872 | 0 .49 RPM |
CEU_NA12873 | 0 .19 RPM |
FIN_HG00183 | 0 .27 RPM |
FIN_HG00277 | 0 .44 RPM |
FIN_HG00315 | 0 .28 RPM |
FIN_HG00321 | 0 .36 RPM |
FIN_HG00328 | 0 .28 RPM |
FIN_HG00338 | 0 .19 RPM |
FIN_HG00349 | 0 .11 RPM |
FIN_HG00375 | 0 .22 RPM |
FIN_HG00377 | 0 .05 RPM |
FIN_HG00378 | 0 .28 RPM |
GBR_HG00099 | 0 .20 RPM |
GBR_HG00111 | 0 .13 RPM |
GBR_HG00114 | 0 .21 RPM |
GBR_HG00119 | 0 .29 RPM |
GBR_HG00131 | 0 .34 RPM |
GBR_HG00133 | 0 .29 RPM |
GBR_HG00134 | 0 .52 RPM |
GBR_HG00137 | 0 .11 RPM |
GBR_HG00142 | 0 .08 RPM |
GBR_HG00143 | 0 .06 RPM |
TSI_NA20512 | 0 .11 RPM |
TSI_NA20513 | 0 .58 RPM |
TSI_NA20518 | 0 .50 RPM |
TSI_NA20532 | 0 .37 RPM |
TSI_NA20538 | 0 .41 RPM |
TSI_NA20756 | 0 .20 RPM |
TSI_NA20765 | 0 .31 RPM |
TSI_NA20771 | 0 .23 RPM |
TSI_NA20786 | 0 .34 RPM |
TSI_NA20798 | 0 .19 RPM |
YRI_NA18870 | 0 .30 RPM |
YRI_NA18907 | 0 .35 RPM |
YRI_NA18916 | 0 .36 RPM |
YRI_NA19093 | 0 .03 RPM |
YRI_NA19099 | 0 .19 RPM |
YRI_NA19114 | 0 .29 RPM |
YRI_NA19118 | 0 .25 RPM |
YRI_NA19213 | 0 .31 RPM |
YRI_NA19214 | 0 .44 RPM |
YRI_NA19223 | 0 .32 RPM |