Sequence
atgc intronic sequence ATGC exonic sequencegtcctttactgtctctctatctttccttactttctcgctttctctcatgcatccattcacagtttatataactatttcccattgatatgttttgcagTATGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCAC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40200.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 3'ss of exon 5
---gtcctttactgtctctctatctttccttactttctcgctttctctcatgcatccattcacagtttatataactatttcccattgatatgttttg-cagTATGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCAC
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acaacacatttgtttttcttttcatgtccaaattgctgcaaaaagttgtaagttcgaactttttgataatacaga-actaactacaatcttatttcatcagTATGGAAAAGACTATGAGTATGATGCCCCTGTCAAGTTGTTGGACAAGCACTTACATGCAATGGCTCAATCACCTGACGAGCAGCTTGTGGTGGTGTCAC
upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 5
----------------------------------------------------------gtcctttactgtctctctatctttccttactttctcgctttctctcatgcatccattcacagtttatataactat--ttcccattgatatgttttgcagTATGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCAC
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gtttatatctacattcccttttcattttgtttctattgtatcgaataattatcaaaatgttctaaatcatttttacaa-tatcctagctatagcagcccttatactgttcagtgatattatttatttaactctgagcttttctgtgttgcttaccagTATGGAAAGGACTATGAATATGATGCACCTGTCAAGTTGTTGGTCAAGCATTTACATGCAATGGCCCAATCACCTGATGAACAGCTGGTGGTGGTATCAC
upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 5
gtcctttactgtctctctatctttccttacttt--ctcgctttctctcatgcatccattcacagtttatat----aactatttcccattgatatgttttgcagTATGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCAC
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--aactaacaatactttgaacatgtataaatgaaatacgcaaatgctaaaggaggattttgtgtttcattctttaggctaattgatgtttgt-tatttatcagTATGGAAAAGATTATGAATATGATGCACCTGTCAAGTTGTTGGTGAAACATTTACATGCGATGGCGGAATCACCTGATGAACAGCTAGTGGTGGTATCAC
upper sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G868913_T01 (Zea mays), 3'ss of exon 2
-gtcctttactgtctctctatctttccttactttctcgctttctctcatgcatccattcacagtttatataactatttcccattgatatgtttt---gcagTATGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCAC
||| | | | |||| || | | | | | || || ||| | ||| ||| | | | | || | | |||||||||||||| || |||| ||| || || |||||||| ||||| || ||| | ||||||||||| ||||| || ||||||||||| || || ||||
tatccactgtgaattgttgcagtttcttttttcaatttaaatttgtggtgtataaattt-tgttctattgaacattgactaactagagtgctatctgtcagTATGGAAAAGACTACGAATATGATGCCCCGGTCAAGCTGTTGGACAAGCATTTGCATGCAATGGCGCAATCATCTGATGAGCAGCTTGTGGTGGTGTCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcatgcatccattcacagtttatataactatttcccattgatatgttttgcagTATGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCAC
agtttatataactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcctttactgtctctctatctttccttactttctcgctttctctcatgcatccattcacagtttatataactatttcccattgatatgttttgcagTATGGAAAAGAATATGAATTTGACGCACCTGTCAAGCTATTGGAGAAACATCTTCATGCAATGGCTCAATCCGTGGACGAGCAGCTTGTTGTAGTTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT