Sequence
atgc intronic sequence ATGC exonic sequence...tgaactaatccaatttttgggcttacttattgttgttttcaaatgatcaagaggaattttatacttatcgctaaggtcttactgtcatgtaatcttgtagATGTCCAAGTCTGCCCCTTCTGATCAGTCCCGGATTAATCTCCTTGACTCAAAAGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G25840.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G25840.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G177970_T01 (Zea mays), 3'ss of exon 10
------------------------tgaactaatccaatttttgggcttacttattgttgttttcaaatgatcaagaggaattttat-acttatcgctaaggtcttactgtcatg----taatcttg----tagATGTCCAAGTCTGCCCCTTCTGATCAGTCCCGGATTAATCTCCTTGACTCAAAAGAT
| || |||| ||| | | || | |||| || | | | | || ||| | ||| || ||| ||| | ||| ||||||||||||||||| ||||| || ||||| || ||||| || |||||| ||||||||
gtgattgacagaactgccagtttagatatgcatttaattattgagttatgttctgagccgattcatattttttctggttacctgattactgtcctctatacatgtaatgtgatgacttctgttttggtgatagATGTCCAAGTCTGCTCCTTCAGACCAGTCTCGTATTAACCTTCTTGACCCAAAAGAT
upper sequence: AT2G25840.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 10
tgaactaatccaatttttgggcttacttattgttgttttcaaatgatcaagaggaattttatacttatcgctaaggtcttactgtcatgtaatct---tgtagATGTCCAAGTCTGCCCCTTCTGATCAGTCCCGGATTAATCTCCTTGACTCAAAAGAT
|| || | || | | | | | || | | | | | ||| ||| | | || ||| | | | | | ||||||||||||||||||| |||| |||||||| || || || || |||||| ||||||||
-cttctgatgt--ctattagacctctctttatttctacttttgtaaatgggtttcttttgttaccgaatgacaattcctttttcatttttcgtttgtctgtagATGTCCAAGTCTGCTTCTTCAGATCAGTCTCGTATCAACCTTCTTGACCCAAAAGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaagaggaattttatacttatcgctaaggtcttactgtcatgtaatcttgtagATGTCCAAGTCTGCCCCTTCTGATCAGTCCCGGATTAATCTCCTTGACTCAAAAGAT
gtcttac putative branch site (score: 3)
aattttatacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaactaatccaatttttgggcttacttattgttgttttcaaatgatcaagaggaattttatacttatcgctaaggtcttactgtcatgtaatcttgtagATGTCCAAGTCTGCCCCTTCTGATCAGTCCCGGATTAATCTCCTTGACTCAAAAGAT
- - - aatccaa
- - - - - - -tttttgg
- - - - - - - - - - - - - - - - - - - tcaaatg
- - - - - - - - - - - - - - - - - - - - - - -atcaaga