Sequence
atgc intronic sequence ATGC exonic sequencegtcgaaagtttatcttttgaatgtttagtttgaactctttgagattttatattcctttgtttaggagtgtctttatctcctcttgattgggagattccttcttttcttttcattttgtgtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
Basic information
| species | Arabidopsis thaliana |
| transcript | AT1G01060.5 |
| intron # | 3 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G01060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os08g06110.2 (Oryza sativa), 3'ss of exon 4
------------------------------------gtcgaaagt--ttatcttttgaatgtttagtttgaactctttgagattttatattcctttgtttaggagtgtctttatctc-ctcttgattgggagattccttcttttcttttc---------------------attttgtgtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
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gtgaattctccacatatatatgtcatatcacaaatagttctatgctattactttctgaatttactttttgtactcactgtgattat-tagctggttaataaatacggctttaattgagttattgatatggatcttgcatcttttttttttcgttttcttgtttgccgtctgatttattctatagAGCATGTTGGGACAAAGACAGCTGTGCAGATCAGAAGTCATGCTCAAAAGTTCTTCACCAAG
upper sequence: AT1G01060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G175265_T01 (Zea mays), 3'ss of exon 3
gtcgaaagtttatcttttgaatgtttagtttgaactctttgagattttatattcctttgtttaggagtgtctttatctcctcttgattgggagattccttcttttcttttcattttgtgtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG--------------------------------------
|||| | | | ||| | | |||| || || | ||||| | | | | | |||||| | || || | | ||| | | | ||| ||| ||||||||||||| || || |||||||||||||| || |||||||||||||| |||
-------------gttttaataagcttgcttgtaaccactgaggatt-attcatgtggatttagt----tttccaattgatactgattgcaa----tttttttgtttcatcaatctccat--agAGCATGTTGGGACAAAGACGGCCGTGCAGATCAGAAGTCACGCTCAAAAGTTCTTCACCAAGGTTCTTTCTCTATCTGATTGGCTAGTGCTCTTGTTTGG
upper sequence: AT1G01060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G014902_T01 (Zea mays), 3'ss of exon 7
gtcgaaagtttatcttttgaatgtttagtttgaactctttgagattttatattcctttgtttaggagtgtctttatctcctcttgattgggagattccttcttttcttttcattttgtgtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
| | | | || | | |||| ||| || | ||||| | |||||| | | | | | | || ||| | | || | ||| ||| ||||||||||||| || || |||||||||||||| || |||||||||||||| |||
---------------------tcatcaatctgtaaccactgaggttt-attcatgtcgatttagt--ttgctttatactgattgcactttgttttgtttgtttggcttctgagttgctccatagAGCATGTTGGGACAAAGACAGCCGTGCAGATCAGAAGTCACGCTCAAAAGTTCTTCACTAAG
upper sequence: AT1G01060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G05410.3 (Glycine max), 3'ss of exon 4
--------------------------------------------------gtcgaaagtttatcttttgaatgtttagtttgaact---ctttgagattttatattcctttgtttaggagtgtctttatctcctcttgattgggagattcc-ttcttttcttttcatttt--gtgtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
|| ||| || | | | | |||| || | || | |||| || | ||| || | ||||||| ||| | || | | || ||||| ||||| || ||| |||| ||||| || ||||||||||| || || ||||| ||||| |||||||||||||| ||||||
gtgatagtgtgtttatcatttctacttgaagatcttctctttttcttcctttctaaacattgg--tgtaacattctagtagaaaatggatcttcatatttgatttattcttgattggatctgtctttttctttattccatggcttggcccccttcttggtgtttcacttctgctgtacagAGCATATAGGAACAAAGACTGCCGTGCAAATCAGGAGTCACGCACAAAAGTTCTTTACAAAG
upper sequence: AT1G01060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G42260.2 (Glycine max), 3'ss of exon 4
gtcgaaagtttatcttttgaatgtttagtttgaactctttgagattttatattccttt--gtttaggagtgtctttatctcctcttgattgggagattccttcttttcttttcattttgt-gtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
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------------------------ctgctct---ctctattggattaaatctgtatataggaataggactactgttttttctcacgccccctgaccctttttggggggttttacttttgttgtgcagAGCATATAGGAACAAAGACTGCTGTACAAATCAGGAGTCATGCTCAGAAATTCTTTACAAAG
upper sequence: AT1G01060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G45030.1 (Glycine max), 3'ss of exon 2
gtcgaaagtttatcttttgaatgtttagtttgaactctttgagattttatattcctttgtttaggagtgtctttatctcctcttgattgggagattccttcttttcttttcattttgt-gtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
|| | ||| | | ||| || | || | | || | ||| | | | | | ||| || ||||| | |||| ||||||| ||||||| ||||| || |||||||||||||| || ||||| |||||||| || || ||||| ||||||
---agaaactgctctctc---tatttgattaaatctgtatataggactactcttttttctcacgc----cccctgccccctttt--ttggggg-------------ttttaattttgttgtgcagAGCATATAGGAACAAAGACTGCTGTGCAAATCAGGAGTCATGCTCAGAAATTCTTTACAAAG
upper sequence: AT1G01060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA16G01980.4 (Glycine max), 3'ss of exon 3
gtcgaaagtttatcttttgaatgtttagtttgaactctttgagattttatattcctttgtttaggagtgtctttatctcctcttgattgggagattcc--ttcttttcttttcattttg--tgtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
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---------------------tttttttttttggttcgttaa---tttatagt----tgatttgatctgtccttttttttattccatggctcgaccccccttcttggtgtttcacttctgctgtacagAGCATATAGGAACAAAGACTGCCGTGCAAATAAGGAGTCATGCACAGAAGTTCTTTACAAAG
upper sequence: AT1G01060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv15s0048g02410.t01 (Vitis vinifera), 3'ss of exon 2
gtcgaaagtttatcttttgaatgtttagtttgaactctttgagattttatattcctttgtttaggagtgtctttatctcctcttgattgggagattcctt-cttttcttttcattttgtg---tgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
| || | |||| || || || | | ||| ||| | ||| | | ||| | |||||| | ||| |||| |||| ||| |||||||||||| || |||||||||||||| || |||||||||||||||||||| ||||| |||||
----------------------atctattatgaataacatggaatgttgt---cttttaattatacttagtctta---cttggagatctgttccttcctttcctttgtttttatttggtggtgtgcagAACATATAGGAACAAAGACTGCTGTGCAAATCAGAAGTCATGCACAAAAATTCTTTTCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttatctcctcttgattgggagattccttcttttcttttcattttgtgtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
tcttgat putative branch site (score: 4)
ttccttcttttctttt putative PPT
ttttcttttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcgaaagtttatcttttgaatgtttagtttgaactctttgagattttatattcctttgtttaggagtgtctttatctcctcttgattgggagattccttcttttcttttcattttgtgtgcagAACATATTGGGACAAAGACTGCTGTTCAGATCAGAAGTCATGCACAAAAGTTCTTCACAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
