Sequence
atgc intronic sequence ATGC exonic sequencegtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os03g60000.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AC217358.3_FGT005 (Zea mays), 3'ss of exon 3
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgcta-gtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
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-----------------------------gtaccattcatgcgtcta-gacacgatgttccccatataacaactgtcttgctagga--------ttggatgagattaggatatgttaacagttcattcatgcattcgattccgatgcagGCTGTGAGCAGGGAGATTAGGAAGATTCTGACTGAGAGGGCCAACAACTTCAATATTGCTCTGGATGATGTGTCCATCACAAGCCTCAGCTTTGGAAAAG
upper sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA11G11670.2 (Glycine max), 3'ss of exon 4
--------------------------------gtactgtcatcatat---ctatctgtgtttaaa-tatctaatatgtttccatggtatgctatgctagtttaagag-ctaatatagtaggatat---ttagt-ttaagagttaa--tatagtaggatatatgctaataattactcctttatccaac------acagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
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gtaaatatttaccagattcttccccatcttctgtacagctagtaactgggctaattgtatgcatgctctgtaattctcagctggagtttgtatcataatcttaggaatctagtaaattcacttttggatgagtattaaaagtgaaattatagccttataagtgggactgattgtttctagaacatactgtttaacagAATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCCTCCCAGTTTAACATTGCTTTGGATGATGTGTCAATCACAAGTTTGACGTTTGGGAAGG
upper sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA12G01850.1 (Glycine max), 3'ss of exon 3
--------gtactgtcatcatatctatctgt-gtttaaatatctaatatgt-----ttccatggtatgc-tatgctagtttaagag--ctaatatagtaggatatttagt-----ttaagagttaa--tatagtaggatatatgctaataattactcctttatccaac------acagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
||| || | |||||| | || | | || | ||| | | ||| | ||| || | | || |||||| | | | || ||| ||| || || | | ||| || | ||||| | || | | || |||| ||| || | || || |||||||| |||| ||||||| | | || ||||||||| ||||||||||||| ||||||||| | | ||||| || |
gtaaatatttaccagattcttccctatcttttgtacagctcattactctgtagttctcacttggagtttgtatcatattcttaggaatctaataaaatcactttttggacgagtactaaaagtgaaattacaaccgtataagtgggactaattgtttctagagcatactgtttaacagAATGTTAGTCGAGAAATAAGGAAGATATTGACTCAGAGGGCGTCCCAATTTAACATTGCTTTGGATGATGTGTCAATCACAAGTTTGACGTTTGGGAAGG
upper sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G03860.3 (Arabidopsis thaliana), 3'ss of exon 4
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
| | | | | | | | || | ||| | || | | | | | | || |||||| | || | |||||||||||| ||||| | ||||| ||||||||| ||||| ||||| |||||||||| |||||||| |||||||| | ||| | || || ||||
--------------------------------------------------------gtacgtatctcaacattctttttctacaactttt---ctgctcttttgtttctaatggtggactctgt---ttactctctcctcta-----gGCTGTGAGCAGAGAGATACGCAAGATTCTGACAGAGCGGGCTTCTAACTTTGACATTGCTCTTGATGATGTCTCCATCACGACTCTGACATTCGGCAAAG
upper sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT2G20530.2 (Arabidopsis thaliana), 3'ss of exon 5
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
|| | || | | | || | | | || | | || ||| | ||||| ||||||||| | | || | ||| ||| | | ||||| || || || ||||| ||||| || || || |||||| ||||||| ||||||||||||||||||||| | | | || ||||| |
----------------------------gttagccaactggctgtaa--atacattttattgattcctcttcaatggtaaattgatgtcccttttaat-------------ggatatatgtt--tttttggtgtttt--tcaa----gTCGGTGAGTAGAGAAATCAGGAAAATCCTAACTCTAAGAGCCGCAAACTTCCACATTGCACTGGATGATGTGTCCATCACAGGCTTGACATTCGGAAAGG
upper sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv19s0085g00730.t01 (Vitis vinifera), 3'ss of exon 5
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
||| || |||||||| || | || ||| || | |||||| | | || | |||||| | | | | || | || | |||||| || |||| || ||||| || | ||| | ||||||| ||||| ||| ||||||||||||||||||||||||||||| ||||| || | ||||| | |
-------------------------------------tattttagcatggtata--ataattgtggaagga-taggttgttaggat-tacgataaaattttaaatatatcaagttctgagcaatccatatgttctttat-------agACTGTTAGTAGGGAAATACGTAAGTTATTGACAGAAAGGGCAGCCAATTTCAACATTGCTCTGGATGATGTGTCCATTACAAGCCTTACTTTTGGGAGGG
upper sequence: LOC_Os03g60000.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv15s0048g02350.t01 (Vitis vinifera), 3'ss of exon 5
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagcta--atatagtaggatatttagtttaagagttaatatagtaggata-tatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
||| || | || ||| | || | | |||| | || | ||| || || || || || | | | | | | | | | | | ||||||| |||||||| || | ||||| ||||||| ||||| ||| |||||||| |||||||||||||||||||||||||| || | ||||| || |
--------------------------------------------------tattttagcttggtgtaataactgtggaagaataggttgttaggatta-gataaaaaattttaaattactgagttctgagcaatttgtatgttctttatagGCTGTTAGCAGGGAAATACGTAAGATATTGACAGAAAGGGCAGCCAATTTCAACATCGCTCTGGATGATGTGTCCATCACAAGCCTTACTTTTGGGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
tgctaat putative branch site (score: 2)
ttactcctttatcc putative PPT
atatatgctaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgtcatcatatctatctgtgtttaaatatctaatatgtttccatggtatgctatgctagtttaagagctaatatagtaggatatttagtttaagagttaatatagtaggatatatgctaataattactcctttatccaacacagGCTGTGAGCAGGGAGATTAGGAAGATCCTGACAGAGAGGGCTAGCAACTTCAACATTGCTCTGGATGATGTGTCCATCACAAGTCTCAGCTTTGGAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT