Sequence
atgc intronic sequence ATGC exonic sequencegtaataaatctgatcattgtgtttaatatttttgagagtgagaatccattcaaatttggtgttaaaagatttttggtttgaaattatattttagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G48100.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G48100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA04G34820.1 (Glycine max), 3'ss of exon 2
-------------------------gtaataaatctgatca-ttgtgtttaatatttttgagagtgagaatccattcaaatttggtgttaaaagatttttggtttga-aattatattt-tagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
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gtgagcaaaatgcaaacttggcttttgaattgttaaaggcacttctttttagtgttttaaacaat-aggtcttacttggaagtgatgcttatg--ttgttattttgatgactgtttcggcagAGTGTGAAGGTTAATTTGATAATGACGGATTATTCCATGCCCGGGATGACAGGATATGAATTGCTCAAGAAGATAAAG
upper sequence: AT3G48100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G01730.1 (Glycine max), 3'ss of exon 2
gtaataaatctgatcattgtgtttaatatttttgagagtgagaatccattcaaatttggtgttaaaagattt-ttggtttgaaattatattttagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
||| | || ||| || || | ||| || || ||||| | ||| ||| || | ||| | || || | | ||| ||||| | |||||||||||||| || ||||| |||||||||||||||||| |||| ||||| |||||
---gtaagtgc-attattatgattttgagtttgttttgtcgttggttgttgaaattggtgcttattttgtttgtttgcttggttgtg-gttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACTGGATATGAATTACTCAAGAAAATCAAG
upper sequence: AT3G48100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G10170.3 (Glycine max), 3'ss of exon 2
gtaa-taaatctgatcattgtgtttaatatttttgagagtgagaatccattcaaatttggtg-ttaaaagatttttggtttga--aattata-ttttagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
|||| | ||| ||| ||| ||||| | | | ||||||||| ||| || || |||||| || | || || | | ||| ||||| | |||||||||||||| || ||||| |||||||| ||||||||| |||| ||||| |||||
gtaagtgaattctgcttttgggttattggcttttgtttggatgttggttgttgaatttggtgcttatgtagttgtttgtttgattggttgtggttacagAGTGTTAAGGTTAATCTCATAATGACGGATTATTCCATGCCGGGGATGACAGGATATGAATTACTCAAGAAAATCAAG
upper sequence: AT3G48100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G19870.2 (Glycine max), 3'ss of exon 1
gtaataaatct-gatcattgtgtt--taatatttttgagagtgagaatccattcaaatttggtgttaaaagatttttggtttgaaattatattt-tagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
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gtaagaaaacttggcttttgaattgttaaaggcacttcttttcaggtt--actcggaagtgaagcttatg--ttgttatttgatgattgttttgacagAGTGTGGATGTTAATTTGATAATGACGGATTATTCCATGCCGGGGATGACAGGATACGAATTGCTCAAAAAGATTAAG
upper sequence: AT3G48100.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv17s0000g07580.t01 (Vitis vinifera), 3'ss of exon 2
gtaataaatctga--tcattgtgtttaatatttttg----agagtgagaatccattcaaatttggtgttaaaagatttttggtttga-aattatattttagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
| || || | || || || ||||| ||||| | | | | | | ||| || || | |||| | | | || || ||| | ||||| | ||| |||| |||||||| || ||||||||||||||||| || ||||| | || |||||||||||
gcaaataaacagaggtctttttgtttttccttttttgattaaattcaaagatttctttaatactgt-ttggatgattgatatctcaatggtttccttgaagGGTTTGAAGGTGAATCTGATCATGACGGACTATTCTATGCCTGGGATGACAGGGTATGAGTTGCTCAAGAAGATCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagaatccattcaaatttggtgttaaaagatttttggtttgaaattatattttagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
tgttaaaagatttttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataaatctgatcattgtgtttaatatttttgagagtgagaatccattcaaatttggtgttaaaagatttttggtttgaaattatattttagGATCTGAAGATTAATTTGATAATGACGGATTACTCTATGCCTGGGATGACTGGATATGAACTACTGAAGAAGATCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA