Sequence
atgc intronic sequence ATGC exonic sequencegtgaatcctcaaaatatccctcttgcttagattatgttgagacgcaatattagtttatgcaattgtacacatgacattctgatcatggtgtttgctcgaatattttccagACATCCAAACCCACATTATCGGATATCAATTTGGAGATACCGGTGGGCAGCTTGGTTGCCATTGTAGGTGGAACTGGAGAAGGTAAGACGTCACTTATTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30420.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: GLYMA06G46940.1 (Glycine max), 3'ss of exon 18
gtgaatcctcaaaatatccctcttgcttagattatgttgagacgcaatattagtttatgcaattgtacacatgacattctgatcatggtgtttgctcgaatattttccagACATCCAAACCCACATTATCGGATATCAATTTGGAGATACCGGTGGGCAGCTTGGTTGCCATTGTAGGTGGAACTGGAGAAGGTAAGACGTCACTTATTT
||| | | | | | || || | || || ||| || | | | || | |||| | || | || | | || | || ||| | ||||| |||||||| ||||||||| |||| ||||| || |||||||| ||||| || | || || ||||||||||| || || ||||||||||
atgagattctatagttttcaattt--tttggatacattt---tataattttgatattagtaact-cacacttcacttcatgcatgaaaactgtattcaa----ttcacagGAAGAGAAACCGACATTATCAGATATCAATGTGGAAATACCAGTTGGCAGCTTAGTTGCAATCATTGGCGGTACTGGAGAAGGCAAAACATCACTTATTT
upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv10s0003g04450.t01 (Vitis vinifera), 3'ss of exon 5
gtgaatcctcaaaatatccctcttgcttag--attatgttgagacgcaatattagtttatgcaattgtacacatgacattctgatcatggtgtttgctcgaatattttccagACATCCAAACCCACATTATCGGATATCAATTTGGAGATACCGGTGGGCAGCTTGGTTGCCATTGTAGGTGGAACTGGAGAAGGTAAGACGTCACTTATTT
|||| || || | | || || ||||||| | | || ||| || |||| | | | || || | ||| | | ||| |||| || |||||||| ||||| ||||||||||||| ||||| || |||||||| ||||| |||| ||| | ||||||||||| ||||| |||||||| |
---aatc--aaagctacaaggaaggatgagctatcatgttgactttctaatgtattttttg----tgtaagaaagcagtcctaatgttcagtttttttt---tttttcccagGCAAAAAAACCCACTTTATCAAATATCAATTTGGATATACCAGTTGGCAGCTTAGTTGCAGTTGTTGGTCGTACTGGAGAAGGAAAGACATCACTTATAT
upper sequence: AT1G30420.1 (Arabidopsis thaliana), 3'ss of exon 16
lower sequence: Vv10s0003g04470.t01 (Vitis vinifera), 3'ss of exon 17
gtgaatcctcaaaatatccctcttgctta-gattatgttgagacgcaatattagtttatgcaa--ttgtacacatgacattctgatc-atggtgtttgctcgaa-tattttccagACATCCAAACCCACATTATCGGATATCAATTTGGAGATACCGGTGGGCAGCTTGGTTGCCATTGTAGGTGGAACTGGAGAAGGTAAGACGTCACTTATTT
|| || | | || | || | | | | || | |||| || | | | | || || | | || || |||||| || | || ||||| ||||| ||||||||||||| ||||| || || ||||| ||||| |||| ||||| ||||||||||| ||||| || || || |
---------------attccaagcaatcatgaaagtttttaaatatattttttttgtatgaaagatagctgttcttaaatcctcttttacagttcttaaatattctattttttagGTAGAGAAGCCCACTTTATCAAATATCAATTTGGATATACCAGTTGGTAGCTTAGTTGCAGTTGTTGGTGGCACTGGAGAAGGAAAGACATCTCTCATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgcaattgtacacatgacattctgatcatggtgtttgctcgaatattttccagACATCCAAACCCACATTATCGGATATCAATTTGGAGATACCGGTGGGCAGCTTGGTTGCCATTGTAGGTGGAACTGGAGAAGGTAAGACGTCACTTATTT
ttctgat putative branch site (score: 3)
tattttcc putative PPT
aatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaatcctcaaaatatccctcttgcttagattatgttgagacgcaatattagtttatgcaattgtacacatgacattctgatcatggtgtttgctcgaatattttccagACATCCAAACCCACATTATCGGATATCAATTTGGAGATACCGGTGGGCAGCTTGGTTGCCATTGTAGGTGGAACTGGAGAAGGTAAGACGTCACTTATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA