RetrogeneDB ID: | retro_mmus_1608 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
Coordinates: | 17:5417511..5418513(-) | ||
Located in intron of: | ENSMUSG00000004945 | ||
Retrocopyinformation | Ensembl ID: | None | |
Aliases: | None | ||
Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
Parental gene symbol: | Ldha | ||
Ensembl ID: | ENSMUSG00000063229 | ||
Aliases: | Ldha, Ldh1, Ldhm, l7R2 | ||
Description: | lactate dehydrogenase A [Source:MGI Symbol;Acc:MGI:96759] |
Percent Identity: | 67.07 % |
Parental protein coverage: | 92.52 % |
Number of stop codons detected: | 0 |
Number of frameshifts detected | 0 |
Parental | SKMATLKDQLIVNLLKEEQAPQNKITVVGVGAVGMACAISILMKDLADELALVDVMEDKLKGEMMDLQHG |
S.MAT.K..LI.....EE....NK...VG.G.VGMACAI.I..K.L.DELALVD..E.K.KGE.MDLQHG | |
Retrocopy | SSMATVKGELIQHISSEEPVLHNKVSIVGTGSVGMACAIGIIAKGLTDELALVDNNEEKMKGETMDLQHG |
Parental | SLFLKTPKIVSSKDYCVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFIIPNIVKYSPHCKLLIVSN |
S.F.K.P.IV.SKD..VTANS..VIITAGARQ...E.RLNLVQRNV.IFK.....I.K.SP.CK...VSN | |
Retrocopy | SVFMKMPNIVCSKDFRVTANSEVVIITAGARQEKNETRLNLVQRNVTIFKAMVAEIIKHSPRCKIIVVSN |
Parental | PVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVHALSCHGWVLGEHGDSSVPVWSGVNVAG |
PVDILT.V.WK.SGFPKNR.IGSGCNLD.ARFRY..G.RLG.H..SCHGWVLGEHGDSSVPVWSGVN.AG | |
Retrocopy | PVDILTFVTWKLSGFPKNRIIGSGCNLDTARFRYMLGQRLGIHSESCHGWVLGEHGDSSVPVWSGVNIAG |
Parental | VSLKSLNPELGTDADKEQWKEVHKQVVDSAYEVIKLKGYTSWAIGLSVADLAESIMKNLRRVHPISTMIK |
V.L..LN...GT..D.E.W..VHK.V..SAY..IK.KGYTSWAIGLSV.D.AESI.KNLR..HP..T.I. | |
Retrocopy | VPLRELNSAIGTSKDPEKWGDVHKEVIASAYNIIKMKGYTSWAIGLSVTDIAESILKNLRKTHPVTTKIQ |
Parental | GLYGINEDVFLSVPCILGQNGISDVVKVTLTPEEEARLKKSADTLWGIQKELQF |
GLYGI.E.VFLSVPCILG..GISD..KV.L.P.EEA...KSA.T.W.IQK...F | |
Retrocopy | GLYGIKEEVFLSVPCILGESGISDIIKVKLSPTEEAQMVKSAETIWKIQKDIKF |
* | Stop codon |
> | Forward frameshift by one nucleotide |
< | Reverse frameshift by one nucleotide |
Library | Retrocopy expression | Parental gene expression |
---|---|---|
SRP007412_brain | 0 .23 RPM | 162 .35 RPM |
SRP007412_cerebellum | 0 .39 RPM | 72 .30 RPM |
SRP007412_heart | 0 .06 RPM | 465 .65 RPM |
SRP007412_kidney | 0 .31 RPM | 344 .67 RPM |
SRP007412_liver | 0 .19 RPM | 394 .74 RPM |
SRP007412_testis | 439 .09 RPM | 722 .17 RPM |
ENCODE library ID | Target | ChIP-Seq Peak coordinates |
---|---|---|
ENCFF001YJZ | POLR2A | 17:5408855..5419001 |
ENCFF001YKA | POLR2A | 17:5419049..5419312 |
ENCFF001YKA | POLR2A | 17:5418449..5418670 |
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_55298 | 1018 libraries | 42 libraries | 6 libraries | 0 libraries | 6 libraries |
Experiment type: | PCR amplification |
---|---|
Forward primer: | GCAGAAGAGTGAGTACAACC (20 nt long) |
Reverse primer: | CACACTTATGAAAGTTAGCCG (21 nt long) |
Anneling temperature: | 55 °C |
(Expected) product size: | 1362 |
Electrophoresis gel image: | |
Additional comment: | Pfu DNA Polymerase; pooled mouse cDNA; 40 cycles of PCR |
Species | RetrogeneDB ID |
---|---|
Rattus norvegicus | retro_rnor_578 |