Sequence
atgc intronic sequence ATGC exonic sequencegtaatctccatttctgtaattttgcaggggatcaggtgatacgtaggtgattcttcagtactttccctacaaaagaacctgactgaggtttgctcttttgtttttgggttctatgctagATGTCAGATCCTTTGACAGCCCTAATGCATGCTGTCCAAGTCATGAACTTCCTCAAGACATTGATCTTGAGGACACTTCGAGAGCGTGACGATGCAGCTA
Basic information
species | Oryza sativa |
transcript | LOC_Os12g34840.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g34840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G323936_T01 (Zea mays), 3'ss of exon 3
gtaatct-ccatttctgtaattttgcaggggatcaggtgatacgtaggtgattcttcagtactttccctacaaaagaacc-tga-----ctgaggtttgctct---------------tttg--tttttgggttctatgctagATGTCAGATCCTTTGACAGCCCTAATGCATGCTGTCCAAGTCATGAACTTCCTCAAGACATTGATCTTGAGGACACTTCGAGAGCGTGACGATGCAGCTA
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gtagtttactattattgcag----gcataggactataggaggtgttccatatgcacatgtacttctcatacaacaaaattgcgagaaatctgtagatcaccctgcttcaacagctaaatttacttttttttgttctatgttagATGTCAGATCCACTGACAGCACTCATGCATGCCGTCCAAGTCATGAACTTTCTCAAGACACTGATCTTGAGGACGCTTCGGGAGCGCGATGATGCAGCCA
upper sequence: LOC_Os12g34840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv07s0104g01120.t01 (Vitis vinifera), 3'ss of exon 3
gtaatctccatttctgtaattttgcaggggatcaggtgatacgtaggtgattcttcag-tactttccctacaaaagaacctgactgaggtttgctcttttgtttttgggttctatgctagATGTCAGATCCTTTGACAGCCCTAATGCATGCTGTCCAAGTCATGAACTTCCTCAAGACATTGATCTTGAGGACACTTCGAGAGCGTGACGATGCAGCTA
| || | | | | | | || || || | | | | | | | | ||| ||| || || | || | | ||||||| ||||| ||||| || || ||||||||||| ||||| |||||||| || ||||| ||||| | ||||| | || || || || |
------------------------gttgatattaaatcttgaaaatttcttgttttagctaatgctttggtccatggatttcaataaatagaactccttttttgtttgatttca--ccagATGTCTGATCCATTGACCGCTCTGATGCATGCTGTTCAAGTGATGAACTTGCTAAAGACCCTGATCACAAAAACACTAAGGGAACGGGAAGAAAGCCCGG
upper sequence: LOC_Os12g34840.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S60_256V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------gtaatctccatttctgtaattttgcaggggatcaggtgatacgtaggtgattctt-----cagtactttccctacaaaagaacctgactgaggtttgctcttttgtttttgggttctatgctagATGTCAGATCCTTTGACAGCCCTAATGCATGCTGTCCAAGTCATGAACTTCCTCAAGACATTGATCTTGAGGACACTTCGAGAGCGTGACGATGCAGCTA
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gtatagtgttgtttctacgcttttcacccagagaagctgatgaccattacaagatcagactcgtagagatttcactacagatgctgtcttcgacgtttcatgtgctgaatttgaacgtaggtattccgtgtttatggtgtttcaattgttgtagaatgtg--taacatttattga--cattgcttcattatccttcagATGGCTGATCCACTGACAGCTCTGATGCATGCTGTTCAAGTCATGAACTTGCTCAAAACTCTGATTCTTCGCACACTGAAGGACCGAAAGGCCACTTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctacaaaagaacctgactgaggtttgctcttttgtttttgggttctatgctagATGTCAGATCCTTTGACAGCCCTAATGCATGCTGTCCAAGTCATGAACTTCCTCAAGACATTGATCTTGAGGACACTTCGAGAGCGTGACGATGCAGCTA
acctgac putative branch site (score: 3)
ttttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctccatttctgtaattttgcaggggatcaggtgatacgtaggtgattcttcagtactttccctacaaaagaacctgactgaggtttgctcttttgtttttgggttctatgctagATGTCAGATCCTTTGACAGCCCTAATGCATGCTGTCCAAGTCATGAACTTCCTCAAGACATTGATCTTGAGGACACTTCGAGAGCGTGACGATGCAGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT