Sequence
atgc intronic sequence ATGC exonic sequencegtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G34410.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 8
gtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaag-tacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
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-----------------------------------------------------------------------gtgagttatgc--atgttttctgtc--ttag-cattattctcattaaccatggataggattttacacc-attttcctttcatgtacagGATATAAGG-ATCCAGAGCCTTCCAAGGCAAACTTACCCCTGCTACATGAGTGGCATTTCCGATCTGGCCTTGATCGATACATATGGATTATTGGAATGAT------
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G076394_T01 (Zea mays), 3'ss of exon 8
gtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
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------------------------------------------------------------------gtaaggtatatatctacgcatcccattgccattttaaatcatggatcaagagtt--gaagattgga-aacaaatgatcttttttgtt---cagGTTACAAAAACCCAGAGCCTTCTAAGATGAACTTACCCCTGTTACACGAATGGCGCTTCCGCTCTGGCCTTGATCGTTACATATGGATCATTGGAATGAT------
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 9
gtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
||| || | | |||| ||| | || || | | | || | ||| | || | || || || | | ||| |||| || |||||||| || || || || || || | | ||||| ||||| |||||||| || ||||| |||||||| ||||| ||||||||||| |||||
------------------------------------------------------------gcttttgtatgttgtctgtttgcaat-tttctagttgatttgctaatataagcttacatgctgtttactg-caaatgcataattgtaatttttatgtgg---cagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 9
gtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
||| || | | | |||| ||| | || || | | | || | ||| | || | || || || | | ||| |||| || |||||||| || || || || || || | | ||||| ||||| |||||||| || ||||| |||||||| ||||| ||||||||||| |||||
------------------------------------------------------------gcttttgtatgtagtctgtttgcaat-tttctagttgatttgctaatataagcttacatgctgtttagtg-caaatgcataattgtaatttttatgtgg---cagGTTATACTGATCCTGCAAAGCCTGATCTCCCTCGAATGCATGAGTGGCATTTCAGATCTGGGCTTGATCGCTACATCTGGATAATTGGAATGATTTATGC
upper sequence: AT2G34410.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S357_34V6.1 (Physcomitrella patens), 3'ss of exon 8
gtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
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----------------------------------------------ggactagttgtgcacc--attcataaattgtgatccttaatttcatggcagtttaatgat--aacctagcgatagt---tgctgagtatt-tttacttatttttgcagCGTAT---CAAGATCCTTT-ATCAAAGCACCCCA----CTCCCTTGCTGCATGAATGGCACTTCAGATCAGGACTGGATCGATACATCTGGATTGTGGGCATGCTCTA--- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
tttttttccttacac CT-rich tract
taacatttagtttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtatcagactcttctcatatcttttactgtgttcggcatggtcgactgcatatccgtcttgtgctaaaaaaatcctgccaatgtttgttgtcacttggtcactggaattagtgtttttgtatgttgactaacatttagtttttttccttacacaagtacagGATACACTGATCCAGCTAAACCAGAACTACCACTTTTACATGAATGGCACTTCAGATCAGGACTTGACCGCTACATATGGATCATTGGAATGATATATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA