Sequence
atgc intronic sequence ATGC exonic sequence...tcttaactccagggattcaattttctttctgtatacgtatgtgtacaaattggaaaaacacgacatcttgatctaatatgttttctcatgtttataacagGTAAATCAGAAGATGATCCTCACTCTAACAGCGAGTATCATGTACTGGAGTCTGCAGCAACCAGTTGAAGAGTTGGAGACATCTTCATCCCCTGCTGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os02g48740.1 (Oryza sativa), 3'ss of exon 14
-tcttaactccagggattcaattttctttctgtatacgtatgtgtacaaattggaaaaacacgacatcttgatctaatatgttttctcatgtttataacagGTAAATCAGAAGATGATCCTCACTCTAACAGCGAGTATCATGTACTGGAGTCTGCA---GCAACCAGTTGAAGAGTTGGAGACATCTTCATCCCCTGCTGATG
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ctgtctacattatttgtt-gtctgtgatcctcttctcttttatcttgaaaaatgatggttattatctgttgactaatcgtactcttatgtttctgtttcagGTAAATCAGAAGATGATCCTAACGCTTACGGCTAGCATCATGTATTGGAGTCTACAGAAGCAACCACAGTCACAATCTGAAACGTCAGAACAATCAGAGC---
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G556845_T01 (Zea mays), 3'ss of exon 13
-----------------------------------------------tcttaactccagggattcaattttctttctgtatacgtatgtgtac----aaattggaaaaacacgacatcttgat-ctaatatgttttct-----catgtttataacagGTAAATCAGAAGATGATCCTCACTCTAACAGCGAGTATCATGTACTGGAGTCTGCAGCAACCAG-----TTGAAGAGTTGGAGACATCTTCATCCCCTGCTGATG
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gtaacaagggaattccatattagttgcacctatgaattcgacaaaaaaatgatatgtaaacaat-aactttcttataaaacaagcttatataaatcaagactaggagcctgcagtaattaaatactgattttttttctatttgcattgtcatggcagGTGAACCCAAAGATGATCCTCACCCTGACAGCAAGCATCATGTACTGGAGCCTGCAGAATCAAGGGCCATACAAGAGTTCAGGACCACAGGATGCTCTTC-----
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G46580.1 (Glycine max), 3'ss of exon 13
tcttaactccagggattcaattttctttctgtatacgtatgtgtacaaattggaaaaacacgacatcttgatctaatatgttttctcatg--tttataacagGTAAATCAGAAGATGATCCTCACTCTAACAGCGAGTATCATGTACTGGAGTCTGCAGCAACCAGTTGAAGAGTTGGAGACATCTTCATCCCCTGCTGATG
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ccatcatgtaataggg-caatgataccaaaaaatttaagttgacacattctggattgagtttgt-ttatgatgtgattgattctctgttgatctcatggcagGTTAATCAGAAGATGATTCTCACTCTTGCAGCCAGTATAATGTATTGGAGCCTGCAACAACAGACTGAAGACACGGATTCATTTCCTTCACCTGTCAACA
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA14G02090.1 (Glycine max), 3'ss of exon 14
tcttaactccagggattcaattttctttctgtatacgtatgtgtacaaattggaaaaacacgacatct-tgatctaat--atgttttctcatgtttataacagGTAAATCAGAAGATGATCCTCACTCTAACAGCGAGTATCATGTACTGGAGTCTGCAGCAACCAGTTGAAGAGTTGGAGACATCTTCATCCCCTGCTGATG
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---tttctcatgtaaaatggcaatgataccaaaaaattaagttgacacattctggatatagtttgtttatgatgtgattgattctttgttgatctcatggcagGTTAATCAGAAGATGATTCTCACTCTTGCAGCCAGTATAATGTATTGGAGCCTGCAACAACAGACTGAGGACATGGATTCATTCCCTTCACCTGCCGGCA
upper sequence: Vv19s0090g01440.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT4G26700.2 (Arabidopsis thaliana), 3'ss of exon 14
tcttaactccagggattcaattttctttctgtatacgtatgtgtacaaattggaaaaacacgacatcttgatctaatatgttttctcatgtttataacagGTAAATCAGAAGATGATCCTCACTCTAACAGCGAGTATCATGTACTGGAGTCTGCAGCAAC--CAGTTGAAGAGTT-GGAGACATCTTCATCCCCTGCTGATG
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-------------gtaagaactgagagactata-atgtat---catcatccgaaatagca-attgctcagatgagatgtgttttggtatgtt-gtgacagGTGAATCAGAAGATGATCCTAATTTTAACGGCAAGTATAATGTACTGGAGTCTTCAGAGACATTCACGGGAGAGTTCAGATTCGTCGTCAACTCAGAGCA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caaattggaaaaacacgacatcttgatctaatatgttttctcatgtttataacagGTAAATCAGAAGATGATCCTCACTCTAACAGCGAGTATCATGTACTGGAGTCTGCAGCAACCAGTTGAAGAGTTGGAGACATCTTCATCCCCTGCTGATG
atctaat putative branch site (score: 3)
atctaatatgtttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcttaactccagggattcaattttctttctgtatacgtatgtgtacaaattggaaaaacacgacatcttgatctaatatgttttctcatgtttataacagGTAAATCAGAAGATGATCCTCACTCTAACAGCGAGTATCATGTACTGGAGTCTGCAGCAACCAGTTGAAGAGTTGGAGACATCTTCATCCCCTGCTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - aactcca
- - - - - - - - - - - - ctttctg
- - - - - - - - - - - - - - - - - - gtatgtg
- - - - - - - - - - - - - - - - - - - - - - acaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaca