Sequence
atgc intronic sequence ATGC exonic sequencegttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10260.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 1
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatg-gtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
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--------------------------------------------------------------------gtggaatttcccgcatgcatgtcatatatt-atgcttgacagaa---tgtagtatgttagtaatttgcttc--ttacgccttttgtcacatgtgtacttggtccagGCAACGATTGGCATTGACTTTCTGTCAAAAACAATGTATCTAGAAGACCGAACTGTACGTTTACAACTCTG
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 1
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcag-aattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggt-gtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
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-----------------------------------------------------------------------ttgttttcttggtatatttttttattccatcaacgattcacaattttta----tgcttcctgctgctagactgctgacaaaattttttgttatgtaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCCTGCAGCTTTG
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 1
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcatt--gtgttcattggatcaaatt-ctgatatta-gttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
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-------------------------------------------------------------------------gtttccttggtatatattt----ttttgttctgtcaaggatccacaatttttattcttcctgctgctagatggctgacaaaatattttgttatctaaatttcagGCAACTATTGGTATTGACTTTTTGTCAAAAACAATGTACCTTGAAGATAGAACTGTTCGCTTGCAGCTTTG
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 1
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggt-gtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
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---------------------------------------------------------------------aattatcttcttcgtaaatttgttttgcacaatgtttccat---ctcccttcccccttttcct--gctagggtcttgacaaatttcttgatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTCTGCAGCTTTG
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 1
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatat-tagttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
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--------------------------------------------------------------------atcttctt--cgtaa--atttgttttgcatttgaatctttacgatctcccttcccccttttcct--gctagggtcttgacaaatttctagatcatcaaaatttcagGCTACTATTGGTATTGACTTCTTGTCAAAAACAATGTACCTTGAAGATCGAACAGTTCGTTTGCAGCTTTG
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 1
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
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-----------------------------------------------------------------------aaaaagaaaaaaaaaattggttt-atctaggtaatctgtctattggagttaaaattttaaattagttacattctcttgatactcctt-tttggtaattgcagGCTACCATTGGGATTGATTTTTTGTCTAAAACGATGTACCTTGAGGATCGAACAATTCGTTTGCAGCTTTG
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: PP1S12_267V6.1 (Physcomitrella patens), 3'ss of exon 2
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
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---------------------------------------------------tgttcatgtg---cgaaaatctgatgc----acgaaaatattg--ttca-atttttcaaaacttcgaagtgttctgt-----------ggttatggtgataacca-aattttatgtttgcagGCGACTATTGGCATTGATTTTCTTTCAAAAACAATGTACCTTGAAGACCGCACCGTGCGGCTACAGCTTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcattgtgttcattggatcaaattctgatattagttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
ttctgat putative branch site (score: 3)
tttttgtt putative PPT
aaattctgatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggatcattttcttctatcccatctcgatcaaaattaattttgatccattgtctgtgagatccacgatcctgttgctgtaatgaatggatcagattcagaattgctagaaactcatagcattgtgttcattggatcaaattctgatattagttatggtgtttttgttgcagGCAACCATTGGAATTGATTTTTTGTCAAAAACAATGTACCTTGAGGATAGGACTGTTCGTCTCCAACTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT