Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgagactactcatggcttcttctatattccaacagatatttgtaccgttatgccatatttgacactcttttccgcataatatcttacgttcagGTCCAATTCGTCCAGTTACAATACATTGGTATATTATGACTAGTCCATTTACTGATGAAGCGACACGAAAATATTTCTCGAGTCACAAGTACTTTGGTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31070.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31070.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g10600.1 (Oryza sativa), 3'ss of exon 5
gtgagtgagactactcatggcttcttctatattccaacagatatttgtaccgttatgccatatttgacactcttttccgcataatatcttacgttcagGTCCAATTCGTCCAGTTACAATACATTGGTATATTATGACTAGTCCATTTACTGATGAAGCGACACGAAAATATTTCTCGAGTCACAAGTACTTTGGTCT---------
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----------------gtaatttagtcaagcatgccattaatggtttctttactctttcttaaaaaatcacatgttcaacatgttaactt-tgtgcaaccccagGTACTCCACA---AATACACTGGTATATAATGACTAGCCCCTTTACTGATGAAGCGACTCGAAAATTTTTTGAAAGCCACAGATATTTTGGCTTAGAGCCTGA
upper sequence: AT1G31070.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 6
gtgagtgagactactcatggcttcttctatattccaacagatatttgtaccgtta-tgccatatttgacactcttttccgcataatatcttacgtt-cagGTCCAATTCGTCCAGTTACAATACATTGGTATATTATGACTAGTCCATTTACTGATGAAGCGACACGAAAATATTTCTCGAGTCACAAGTACTTTGGTCT
|| || || | | || || | ||| | | ||| | ||| ||| | | | || ||| | | | | |||| |||||| ||||| || |||||||||||||| |||||||| || ||||| |||| || ||||| || | ||||||||
--------------------------gtaagtttcatttg-tcttggttcagtttctctcgcattatttggttagatcctcattagtttatgtattgcagATTCTTCTTCTTCAGTGCAAATACACTGGTACATCATGACTAGTCCATTCACTGATGAGGCAACACGCAAATTCTTTGAAAGTCATAAATTTTTTGGTCT
upper sequence: AT1G31070.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 5
gtgagtgagactactcatggcttcttctatattccaacagatatttgtaccgttatgccatatttgacactcttttccgcataatatcttacgttcagGTCCAATTCGTCCAGTTACAATACATTGGTATATTATGACTAGTCCATTTACTGATGAAGCGACACGAAAATATTTCTCGAGTCACAAGTACTTTGGTCT
| || || |||| |||| | ||||| || | |||||||| || | || | | |||| | |||| || | || || |||| |||||||| |||||||| ||||||||||||||||| | || || |||| ||| || || || |||||||| ||
--------------gtaagg-ttattctgcattc-------tgtttgt----ttgtatttcatttgacatgctgcccttattattttattacttgcagGCTCAGGTGGTTTTGTGCCAATTCATTGGTACATTATGACGAGTCCATTTACTGATGATGTCACCCGCAAATTTTTTGAAAGCCATAAATACTTTGGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgtaccgttatgccatatttgacactcttttccgcataatatcttacgttcagGTCCAATTCGTCCAGTTACAATACATTGGTATATTATGACTAGTCCATTTACTGATGAAGCGACACGAAAATATTTCTCGAGTCACAAGTACTTTGGTCT
atcttac putative branch site (score: 3)
ataatatctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgagactactcatggcttcttctatattccaacagatatttgtaccgttatgccatatttgacactcttttccgcataatatcttacgttcagGTCCAATTCGTCCAGTTACAATACATTGGTATATTATGACTAGTCCATTTACTGATGAAGCGACACGAAAATATTTCTCGAGTCACAAGTACTTTGGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC