Sequence
atgc intronic sequence ATGC exonic sequencegttagttgcttgtggggaagaaagaatcatcgtatctctagatgtaataactaaatttggtattggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G07690.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G450055_T01 (Zea mays), 3'ss of exon 17
gttag---ttgcttgtggggaaga-aagaatcatcgtatctctaga--tgtaataactaaatttggtattggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA
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gttagcctttgcatccccagagtacaaaattcagtggcccttgaaatttgcgttttctgaatgccct-ccattttatcccgacagCAAGCGGAAGCACAGATAAAGCGAAGAATGGGCATTGGAAGCCACATATCTGAGCGACGGCTGATTGATGGACTAAACAGGATGGGAATGAACGAATCCA
upper sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GRMZM2G075978_T01 (Zea mays), 3'ss of exon 17
---gttagttgc-ttgtggggaagaaagaatc-----atcgtatctctagatgtaataactaaatttggta---ttggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA
|| |||| | ||| | | | ||| || | | || | | | | ||| | || | | | |||||||||||| |||| ||||||||||||||||| ||||| | |||| ||| || | ||||| || ||||| | ||||| ||||| || || |
gttagtatttgcatcccagggtatacaaaattcagctattgaaccttgcattttcctgaacggctttcatcatttttttttcatctgacagCAAGCGGAGGCACAAATAAAGAGAAGAATGGGCATCGGCAGCCACATATCCGAGCGACGGCTGATTGATGATCTAAACCGGATGGGGATGAATGAATCCA
upper sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA17G11220.1 (Glycine max), 3'ss of exon 16
gttagttgcttgtggggaagaaagaat-catcgtatctctagatgtaataactaaatttggtattggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA
||| || |||||| | | ||| | || ||||| | ||||| | ||| || | | |||||||| ||||||||||||||||||||||| || || ||| | |||| || ||||| ||||| || || || |||||||| ||||| || || |
gtttgt--cttgtgatagacatagaccgtcttgttcatctagct-taatatcctaatggattactttacattgtgagcagCAAGCTGAAACACAGATAAAGAGAAGAATTGGAATTGGAAACCACATATCGGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA
upper sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA13G22420.1 (Glycine max), 3'ss of exon 16
gttagttgcttgtggggaagaaaga--atcatcgtatctcta---gatgtaataactaaatttggtattggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA
||| || |||||| || | ||| ||| | | | || || || | || || | | |||||||| ||||| ||||||||||||||||| ||||| ||| | ||||||| ||||| ||||| || || || |||||||| ||||| || || |
gtttgt--cttgtgataaacatagaccatcttgttttttccgtctagcttagtatcctaacggattactttacattgtgagcagCAAGCTGAAACTCAGATAAAGAGAAGAATTGGGATTGGAAACCACATATCAGAAAGAAGGCTGATTGATGACCTCAGCAGAATGGGGATGAATGAATCTA
upper sequence: AT2G07690.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv11s0149g00130.t01 (Vitis vinifera), 3'ss of exon 16
gttagttgcttgtggggaagaaagaatcatcgtatctctagatgtaataactaaatttggtattgg--tgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA----
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----gtgattgacaccctcacctccattttctcttttctttgtttcttatttttactaacacttgggttccccatgaacagcaagCTGAAACACAGATAAAGAGAAGAATGGGAATTGGAAGCCACATATCGGAGAGACGGCTGATTGATGATATGACCAGGATGGGAATGAATGAATCTATTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcatcgtatctctagatgtaataactaaatttggtattggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA
atgtaataactaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttgcttgtggggaagaaagaatcatcgtatctctagatgtaataactaaatttggtattggtgtgaaaaaacagCAAGCGGAAACACAGATAAAGAGAAGAATGGGGATCGGAGCTCGATTATCAGAGAGAAGACTGATAGAGGATCTGGCTAGAATGGGAATGAACGATTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT