Sequence
atgc intronic sequence ATGC exonic sequencegtgggcaacactttttttattgtttggcttgcagtcagctttcgtttcattttacatttggtttaacatggccatgttcgtttagGTGTGTGCATATAAAGATGGGAAAGTCATAATTGACACTGCTGCTGGAGTGCTTGGAAGATATGACCCTCGTCCAGTTCAACCCGATAGTTTATTTCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G24810.2 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G140917_T01 (Zea mays), 3'ss of exon 15
gtgggcaacactttt---tttattgtttggct-tgcagtcagc--tttcgtttc--attttacatttg-gtttaacatggccatgttcgttt------agGTGTGTGCATATAAAGATGGGAAAGTCATAATTGACACTGCTGCTGGAGTGCTTGGAAGATATGACCCTCGTCCAGTTCAACCCGATAGTTTATTTCCTG
|| || | | | | ||| || || || | |||| || || |||| ||||| || || | | || |||| |||| || |||||||||||||| || |||||||| || ||||||||||| |||| || | ||||| || || || |||||||| ||| | | |||||||
gtaggagtctcctaagaatctatgattcaactacgctggcagcaattctgtacaaaatttagtatttgtgtgtataacacttacatttgtttttccctagGTCTGCGCATATAAAGATGGAAAGGTCATAATAGATACTGCTGCTGGTATGCTGGGGAAGTATGATCCCCGACCTGTTCAACCTGATTCTCTTTTTCCTG
upper sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GLYMA14G20110.1 (Glycine max), 3'ss of exon 14
----------gtgggcaacactttttt--tattgtttggcttgcagtcagctttcgtttcattttacatttggtttaaca---tggccatgttcgttt--agGTGTGTGCATATAAAGATGGGAAAGTCATAATTGACACTGCTGCTGGAGTGCTTGGAAGATATGACCCTCGTCCAGTTCAACCCGATAGTTTATTTCCTG
|||| | || | | | | || |||| || | || | || ||| || | | | ||| || || |||| ||||| || |||||||| | ||||| |||||||||||||| ||||||||||| | |||||| || ||||| ||| | || ||||| | ||||| |
gtctattattgtggttgttgttgcattgatgtcaagagccaatcaaatagctcaagtat--ttgttcaattgtcttgataaattctgcataatcacttgaagGTATGTGCCTACAAAGATGGAGAGGTCATTATTGACACTGCTGCAGGAGTGCTTGGTAAATATGATCCACGTCCGGTTAAGCCTGATAGCCTTTTTCCGG
upper sequence: AT5G24810.2 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv04s0008g02740.t01 (Vitis vinifera), 3'ss of exon 13
-------------gtgggcaacactttttttattgtttggcttgcagtcagctttcgtttcattttacatttggtttaacatggccat-----gttcgtttagGTGTGTGCATATAAAGATGGGAAAGTCATAATTGACACTGCTGCTGGAGTGCTTGGAAGATATGACCCTCGTCCAGTTCAACCCGATAGTTTATTTCCTG
|| | || ||||| ||| || ||| | ||| || | || | ||| |||| | || || | || |||| ||||| || ||||||||| | || || ||||| ||||||||||||||||||||||||||||| ||||||||||||||||| ||||| |||||||||
tgctaagtttaatttgtgttgcattttttacattcaaaagcaagcaattggctcaaactttctgttg-acttga--taacttcttcactgatggtgccttaagGTATGTGCCTACAAAGATGGGGAGGTTATTATTGATACTGCTGCTGGAGTGCTTGGAAGATATGATCCTCGTCCAGTTCAACCTGATAGCCTATTTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcagtcagctttcgtttcattttacatttggtttaacatggccatgttcgtttagGTGTGTGCATATAAAGATGGGAAAGTCATAATTGACACTGCTGCTGGAGTGCTTGGAAGATATGACCCTCGTCCAGTTCAACCCGATAGTTTATTTCCTG
gtttaac putative branch site (score: 3)
ttcgttt putative PPT
tttcattttacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgggcaacactttttttattgtttggcttgcagtcagctttcgtttcattttacatttggtttaacatggccatgttcgtttagGTGTGTGCATATAAAGATGGGAAAGTCATAATTGACACTGCTGCTGGAGTGCTTGGAAGATATGACCCTCGTCCAGTTCAACCCGATAGTTTATTTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA