Sequence
atgc intronic sequence ATGC exonic sequencegtagatcttctgattttaaccatttgagttttggatacgttggtttatgtgtgaatgaacttttgacatttttgaattcttggcagACACTTCGTCGACTTGCTCAGAACCGGGAGGCTGCTAGGAAAAGTCGGTTGAGGAAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G68640.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G68640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G10830.2 (Glycine max), 3'ss of exon 5
gtagatcttctgattttaaccatttgagttttggatacgttggtttatgtgtgaatg--aacttttgacatttttgaat---tcttggcagACACTTCGTCGACTTGCTCAGAACCGGGAGGCTGCTAGGAAAAGTCGGTTGAGGAAAAAG---------------------
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------------gttgtgttttcttacaacttgtagctactggtttgtgtttcattactgatgcgttgtttgtttggatgcccttttctagACCCTTCGTAGACTGGCTCAGAATCGGGAGGCTGCAAGGAAAAGTCGGTTAAGGAAAAAGGTAATTGCTTCAAAGTATTAA
upper sequence: AT1G68640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G21020.1 (Glycine max), 3'ss of exon 4
--------gtagatcttctgattttaaccatttgagttttgg-atacgttggtttatgtgtga--atgaacttttgacatttttgaattc---ttggcagACACTTCGTCGACTTGCTCAGAACCGGGAGGCTGCTAGGAAAAGTCGGTTGAGGAAAAAG
| ||||| | || | || | || | | || ||| ||| | | | || || | || | || | || |||| |||||| |||| |||||||| ||||||||||| ||||||||||| || |||||||||
tcaaacctggagatcaaaaggttgtgtttggttacgacttagtagctactgatttgtgtttcattactaatgctttgtttgttcggatgcccttttctagACCCTTCGTAGACTGGCTCAGAATCGGGAGGCTGCAAGGAAAAGTCGATTAAGGAAAAAG
upper sequence: AT1G68640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA10G42280.1 (Glycine max), 3'ss of exon 5
gtagat--cttctgattttaaccatttgagttttggatacgttggtttatgtgtgaatgaacttttgacatttttgaattcttggc---agACACTTCGTCGACTTGCTCAGAACCGGGAGGCTGCTAGGAAAAGTCGGTTGAGGAAAAAG
|| | | || || | || ||| | || || | || | ||| ||| || ||| ||||| ||| |||| | ||| | || |||||||| || |||||||||||||| ||||||||||||||||||
gttgttagctgcttgcatcaaaaccttgtgcttattat-tacttcttgttttgttgttgatagcttactttttgtgaatgctttcttttagACCGTACGTAGGCTAGCTCAGAATCGTGAGGCTGCTAGGAAGAGTCGGTTGAGGAAAAAG
upper sequence: AT1G68640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ28227 (Selaginella moellendorffii), 3'ss of exon 2
gtagatcttctgattttaaccatttgagttttggatacgttggtttatgtgtgaatgaacttttgacatttttgaattcttggcagACACTTCGTCGACTTGCTCAGAACCGGGAGGCTGCTAGGAAAAGTCGGTTGAGGAAAAAG
| || |||||||||| || ||||| |||||||| ||||| || ||||||| || ||||||||||||
---------------------------------------------------------------------------gtgatt--tagacacttcgacgtcttgcacagAACCGCGAGGCCGCACGGAAAAGCCGCTTGAGGAAAAAG
upper sequence: AT1G68640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ29724 (Selaginella moellendorffii), 3'ss of exon 2
gtagatcttctgattttaaccatttgagttttggatacgttggtttatgtgtgaatgaacttttgacatttttgaattcttggcagACACTTCGTCGACTTGCTCAGAACCGGGAGGCTGCTAGGAAAAGTCGGTTGAGGAAAAAG
| | ||| || | | | || | | | || | | | ||| | | | | | | |||||||||| || ||||| |||||||| ||||| || ||||||| || ||||||||||||
---gtacgcctggcactacatttcgctgcaacagcaacttcagggtttgatcgtgtcattgtttctcgtgctggtgattt----agACACTTCGACGTCTTGCACAGAACCGCGAGGCCGCGCGGAAAAGCCGCTTGAGGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggatacgttggtttatgtgtgaatgaacttttgacatttttgaattcttggcagACACTTCGTCGACTTGCTCAGAACCGGGAGGCTGCTAGGAAAAGTCGGTTGAGGAAAAAG
ttttgac putative branch site (score: 3)
ttctt putative PPT
atttttgaattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatcttctgattttaaccatttgagttttggatacgttggtttatgtgtgaatgaacttttgacatttttgaattcttggcagACACTTCGTCGACTTGCTCAGAACCGGGAGGCTGCTAGGAAAAGTCGGTTGAGGAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT