Sequence
atgc intronic sequence ATGC exonic sequence...ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcactactgttatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G28080.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: LOC_Os02g15660.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------------------------ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcac-tactgttatgtttctttt--cagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
| | || | | || | || | | || | || || ||| | || ||| | | | | || | |||||| | || ||||||||||| || |||||||| |||||||||||||| ||| | ||||| |||||||| || || || |||||||| | |||||| ||| || || ||||
gtttgcaaccctatctgttttagttctcaattgagttccgacacatacagtagtctaattcatggccacatcagttttgatgttcacactcgttttgctgggaactatgag-aaccattccctttcatgatccaaagaaaacttgagactgaaaactcatcttatatatcttgatgtttttattgacagACTGCTGCTAGTTACCATGCTATTGCTATTGCTCTGTCTTTAATGGAAGCATACTCTTTAAGTGTCCAACATGAAAAAACCACTTTACGAATACTTCAAG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G318635_T01 (Zea mays), 3'ss of exon 19
ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcactactgttatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
| ||| | | || | | | | | || || | || || ||| | | | || ||| | |||||||| ||||| || ||||| |||||||||||| | ||| | ||||| || ||||| ||||| || |||||||| ||||||| ||| ||| || ||||
gttttgatctgtacacttctaacagttagagtacctgtctgtgatttaaacaaaggctaacatcgaaaggccatcttatgtctcaatattttaatgacagACTGCGGCAAGTTATCATGCTATTGCTATTGCTTTGTCTTTAATGGAAGCGTACTCATTGAGTGTCCAACATGAAAAGACCACGCTAAGGATACTTCAAG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 19
ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcactactgttatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
|| || | | || | || |||| | ||||||||||||||||||||| ||||| || ||||||||||||||| ||||||| |||||||| | || ||||| ||||| |||||||| || || || || || |
--------------------------------------------------gtagttggcatttttaact-----tgttttataattatttactttttcagACTGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAAATCCTGCAGG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 17
------ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcactactgttatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
|| | | | | || | || | | || || | || || | || || | | || | || |||| | || ||||| || ||||| ||||||||||| ||||| || ||||||||||||||| ||||||| |||||||| | || ||||| ||||| |||||||| || ||||| || || |
tcactaaaagcacttcctcatg--ttcagtttcttcacaaatatgcatcagagagggtagttggcatttttaac--ttgttttactatttttttgtttatt--cagACGGCTGCAAGCTATCATGCAATAGCTATTGCTCTTTCTTTGATGGAAGCATACTCTCTAAGTGTTCAGCATGAACAGACCACCCTCCAGATCCTGCAGG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: PP1S73_28V6.1 (Physcomitrella patens), 3'ss of exon 14
--ttcccattctatgaaggcttaggcttaat--aagtaaaatttaccatggaagctaaatgatacgctaaaac-atgaattcactactgttatgtttctttt-cagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
| | | | || || | |||| || | | ||| ||| ||| || |||| |||| | | |||| || |||||||||||||| ||||| || ||||| ||||| ||||| || ||||| || |||||| | || ||||| |||||||| || || |||||||| | |||
gttcgttgtaacactagttgttgaatttttttcgagtacaagtcgtt-tcatctttaacacttaccctatcactgcaaatttactaattgagtacttctgttgcagACTGCTGCAAGTTACCACGCAATTGCAATTGCGCTTTCACTTATGGAGGCTTACTCCCTCAGTGTTCAGCATGAGCAAACTACCTTACAGATTTTGCAAA
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: EFJ08067 (Selaginella moellendorffii), 3'ss of exon 19
ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcactactgt-tatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
| | | || | || | ||| | | | | |||| |||||||| |||||||||||||| |||||||| || || || |||||||| ||||| | | || || || || || || || || || || | ||||
-------------------------------------------------gtgatactatctcaaacaaaacaaatcagttttcatctggagtactttacagACTGCAGCAAGCTACCATGCAATTGCTATAGCACTCTCACTGATGGAAGCATATACACTCAGTGTCCATCACGAACAAACTACGTATCAAATCTTGCAAG
upper sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 19
ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcactactgt-tatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
| | | || | || | ||| | | | | |||| |||||||| |||||||||||||| |||||||| || || || |||||||| ||||| | | || || || || || || || || || ||| | ||||
-------------------------------------------------gtgatactatctcaaacaaaacaaatcagttttcatctggagtactttacagACTGCAGCAAGCTACCATGCAATTGCTATAGCACTCTCACTGATGGAAGCATATACACTCAGTGTCCATCACGAACAAACTACGTATCAAATTTTGCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaagctaaatgatacgctaaaacatgaattcactactgttatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
cgctaaa putative branch site (score: 3)
ttatgtttcttttc putative PPT
taaatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcccattctatgaaggcttaggcttaataagtaaaatttaccatggaagctaaatgatacgctaaaacatgaattcactactgttatgtttcttttcagACTGCTGCAAGCTACCATGCCATTGCTATTGCTCTTTCTCTGATGGACGCATACTCCTTGAGCGTTCAACATGAGCAGACCACTCTACAGATTCTACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - -aagtaaa
- - - - - - - - - - - - - - - - - - - - - - - -aagctaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaac