Sequence
atgc intronic sequence ATGC exonic sequencegtaaataaaatttagactcgagatattttatttagttgttttaaaaatttgattttgaagttgattcctggttttgatgtagGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G61160.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G61160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G40150.1 (Glycine max), 3'ss of exon 4
------------------------------gtaaataaaatttagactcgagatattttatttagttgttttaaaaatttgattttgaagttgattc--------ctggttttgatgtagGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
|| | || | | | | || | | |||| | || ||| | | || | || ||| |||||||||||||| | || || | ||| ||| |||||||| |||||||| || ||||||||||| || || || ||||| ||| | |||||||||||||| |
gtattgatatttattttgcagtatttctttactcgtaggaattgatcctttgcttcactgttctatgggtttatctagttactttctttgcttatccacttcgctttgaatttactgtagGCTAAGTGCCTTGAAACTGGTGAAGCAGTTGCAATAAAAAAAGTGTTGCAAGACAAGAGATATAAGAATAGGGAACTGCAGGTTATGCGAATGCTTGACC
upper sequence: AT3G61160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S306_43V6.2 (Physcomitrella patens), 3'ss of exon 4
---------------------------------------------------------------------------------------gtaaataa-aatttagactcgagatattttatttagttgttttaaaaatttgattttgaagt---------tgattcctg-gttttgatgt--------agGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
|| || || | | || || || | | || | | || ||| ||||| || || || |||| |||| || ||| | || || | || | || || |||||||||||||| |||||||| |||||||| || |||| || |||||||||||| || | || |
gtgattgttaggattaagctctgttcaatttggcgctgtaacgaattctcctttccgctcagacagacctcgtatggaatctggtgtgtggtccgcgatggaggtttcgcacatgtttgttcgcctctcggaatagctcatacggaaagataactgaatgatttttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGTTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
upper sequence: AT3G61160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 3'ss of exon 3
------gtaaataaaatttagactcgagatatttt-------atttagttgttttaaaaatttgattttg---aagttgattcctggttt-tgatgt-agGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
| | ||| | | | | |||| || | | | | || | | | || | ||| | | | | || || |||| || ||| | || || | || | || || |||||||||||| | |||||||| |||||||| || |||| || |||||||||||| || | || |
tacgttgcggaggaaagtccaaatggttatatgtttaccctaacctcatgctggtagagggatagctgtgtctgacttgcgtgttaatgtgtgttgccagGCAAAATGCATCGAAACTGGGGAGACGGTGGCTATAAAGAAAGTGCTGCAGGACAAAAGATACAAGAATCGAGAGCTGCAGATCATGCGACTGTTGGACC
upper sequence: AT3G61160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------gtaaataaaatttagactcgagatattttatttagttgttttaaaaatttgattttgaagttgattcctggttttgatgt-agGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
| || | | | || || | | || | || | || ||| || | ||||| ||| |||| || ||| |||||| | ||||| || || || ||||| ||| | ||||||||||||||||| ||| ||||||||||||||||||| |||| || |
taacttcactggagccagacatggggctgatctgtccatgtgacgttcaaggtggtagaactaggggat--gttctgatcgcgaggg-taattttgttgtcagGCAAAATGCATAGAGAGCGGAGAAACTGTGGCTATTAAGAAGGTGCTTCAGGACAAGAGATACAAGAACCGAGAACTTCAGATCATGCGGCTGCTGGAGC
upper sequence: AT3G61160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ10962 (Selaginella moellendorffii), 3'ss of exon 3
gtaaataaaatttagactcgagatattttatttagttgttttaaaaatttgattttgaagttgattcctg----gttttgatgtagGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
| | | | | ||||| ||| | | | ||| |||||| | || | |||| |||||| | || || | ||| | || || || ||||| ||||||||||||||||||||||||||| | || || || || ||||| | ||||| |
-------------------------gtgtgcaaactcgctttaatcattctaggctaacgtttcttcctgttgggcttcacttcagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCCATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC
upper sequence: AT3G61160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: EFJ04915 (Selaginella moellendorffii), 3'ss of exon 3
gtaaataaaatttagactcgagatattttatttagttgttttaaaaatttgattttgaagttgattcctg----gttttgatgtagGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
| | | | | ||||| ||| | | | ||| |||||| | || | ||||| |||||| | || || | ||| | || || || ||||| ||||||||||||||||||||||||||| | || || || || ||||| | ||||| |
-------------------------gtgtgcaaactcgctttaatcattctaggctaacgtttcttcctgttgggcttcactttagGCCAAGTGCCTCGAAACAGGAGAGACGGTGGCTATCAAGAAGGTGTTACAGGACAAGAGATACAAAAACCGGGAGCTGCAAATAATGCGCCTTCTTGACC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttagttgttttaaaaatttgattttgaagttgattcctggttttgatgtagGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
ttttgat putative branch site (score: 4)
ttttaaaaatttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaataaaatttagactcgagatattttatttagttgttttaaaaatttgattttgaagttgattcctggttttgatgtagGCTAAGTGCTTAGAGACGGAAGAAAAAGTAGCAATAAAGAAAGTGTTACAGGACAAGAGATACAAAAACAGAGAACTTCAGATCATGCGAATGCTTGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA