Sequence
atgc intronic sequence ATGC exonic sequence...aatattgaagggccgatagattatgtatcttacgcttatatgtatttcaatacttaacacgtattactttattttgtgtttgttttgtgacatataccagGTCTGGGCAAGAATATGGTCTGTCCTTGCCGAACATTTCGTATCTGCTGGTAGCCATCATGATGAAAAGATTGCAATGTATGCCATAGATTCTCTGAGAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G43300.2 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 22
aatattgaagggccgatagattatgtatcttacgcttatatgtatttcaatacttaacac--gtattactttattt-tgtgtttgttttgtgacatataccagGTCTGGGCAAGAATATGGTCTGTCCTTGCCGAACATTTCGTATCTGCTGGTAGCCATCATGATGAAAAGATTGCAATGTATGCCATAGATTCTCTGAGAC
|| | || | || || ||| | ||| || || | || | | | | | | |||| | | | |||| | | | ||||||||||| ||||| ||||||||||| || | || || |||| || || || ||||||||||| || ||||| |||||||||||||||||||| ||||
-atctgtaaacattatca--ttgtgcttctatcccttgtaataatattgtcttttgatgctgctctgaatgcatttctaagctctaattgttatgtttttcagGTCTGGGCTAGAATCTGGTCTGTCCTAGCAAATCACTTTATATCAGCAGGGAGTCATCATGATGAGAAAATTGCTATGTATGCCATAGATTCTCTAAGAC
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 22
aatattgaagggccgatag-attatgtatcttacgcttatatgtatttcaatacttaacac--gtattactttattt-tgtgtttgttttgtgacatataccagGTCTGGGCAAGAATATGGTCTGTCCTTGCCGAACATTTCGTATCTGCTGGTAGCCATCATGATGAAAAGATTGCAATGTATGCCATAGATTCTCTGAGAC
| || ||| ||| || || | | | || || | || | | | | | | |||| | | | || | | | ||||||||||| ||||| ||||||||||| || | || || |||| || || || ||||||||||| || ||||| |||||||||||||||||||| ||||
----atctgttaccaatatcattgtgcttccatctcctgtaataatattttcttttgatgctgctctgaatgcatttctaagctctcgttattatgcttttcagGTCTGGGCTAGAATCTGGTCTGTCCTAGCAAATCACTTTATATCAGCAGGGAGTCATCATGATGAGAAAATTGCTATGTATGCCATAGATTCTCTAAGAC
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 22
---aatattgaagggccgatagattatgtatcttacgcttatatgtattt-caatacttaacacgtattactttattttgtgtttgttttgtgacatataccagGTCTGGGCAAGAATATGGTCTGTCCTTGCCGAACATTTCGTATCTGCTGGTAGCCATCATGATGAAAAGATTGCAATGTATGCCATAGATTCTCTGAGAC
||| || | | | || | ||| | | || | ||| | |||| | ||| | | || |||| | ||| |||||| ||||||||||| ||||||||||||||||| || | ||||| |||||||||| ||||||||||| || || ||||| |||||||| ||||||||||| || |
atcaattttcttgaggtta-agctaatgctttctttagttgtttgtgcctattgcacttg---tttgttaatgttttaaaagtttttattgatacatatttcagGTCTGGGCTAGAATATGGTCTGTCCTAGCTAATCATTTTATATCTGCTGGGAGCCATCATGACGAGAAAATTGCTATGTATGCTATAGATTCTCTAAGGC
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 21
lower sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------------aatattgaagggccgatagattatgtatctta-cgcttatatgtatttcaatacttaacacgtattactttattttgtgtttgttttg----tgacatatac-----cagGTCTGGGCAAGAATATGGTCTGTCCTTGCCGAACATTTCGTATCTGCTGGTAGCCATCATGATGAAAAGATTGCAATGTATGCCATAGATTCTCTGAGAC
|| |||||| | | |||| | |||| || | | |||| || || || | | ||| ||| | || | || || ||| | || ||||| |||| | ||||||| | || || | ||||| || | || || ||||| | |||||||||||||||||||| || ||||||||| |||| |
gtaactactcctacatcctagtgtatgttgtttaaaattgaa---tcatcatgttatttcacttaatattttcacat-tttctccacccaatacatga-agtttttttggagtgtcttatgaatctgatgtccacaactacagGTGTGGGGCAAAATATGGGCAGTACTCTCGTTGCATTTTGTTGCGGCAGGGAGCCACGACGATGAAAAGATTGCAATGTACGCTATAGATTCTTTGAGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcaatacttaacacgtattactttattttgtgtttgttttgtgacatataccagGTCTGGGCAAGAATATGGTCTGTCCTTGCCGAACATTTCGTATCTGCTGGTAGCCATCATGATGAAAAGATTGCAATGTATGCCATAGATTCTCTGAGAC
acttaac putative branch site (score: 3)
tattactttattttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatattgaagggccgatagattatgtatcttacgcttatatgtatttcaatacttaacacgtattactttattttgtgtttgttttgtgacatataccagGTCTGGGCAAGAATATGGTCTGTCCTTGCCGAACATTTCGTATCTGCTGGTAGCCATCATGATGAAAAGATTGCAATGTATGCCATAGATTCTCTGAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttaacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg