Sequence
atgc intronic sequence ATGC exonic sequencegtaagcacatccccactcttcttgttcttccttgtagttttttcatggtgtgactaatttcatctgatctttaatagCATCATGGGCTATATCTGTGTATTACGCCTACCAGCGTACCTGGAAGCCGTTCAATCCAATTCTCGGTGAGACTTATGAGATGACTAATCATAATGGGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G02100.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g16690.1 (Oryza sativa), 3'ss of exon 4
gtaagcac-atccccactcttcttgttcttccttgtagttttttcatggtgtgactaatttcatctgatctttaatagCATCATGGGCTATATCTGTGTATTACGCCTACCAGCGTACCTGGAAGCCGTTCAATCCAATTCTCGGTGAGACTTATGAGATGACTAATCATAATGGGAT
||||| || | ||| | | | | || | | | | || ||| ||| | | | ||| ||| |||||||| |||| || || | || |||||||||||||||||||| |||||||| || || || ||||| ||||||||| ||| || | || ||
gtaagttttgcaccttcccttgtgagcaatgcctttaatatccttgttgtttgatct-tttaacttaactttt--cagCTGCATGGGCTGTATCGGTCTACTTTGCATACCAGCGTACCTGGAAGCCTTTCAATCCCATCCTTGGGGAGACATATGAGATGGTTAACCACCAGGGTAT
upper sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S148_87V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------gtaagcacatccccactcttcttgttcttccttgtagttttttca-tggtgtgactaatttcatctgatctttaatagCATCATGGGCTATATCTGTGTATTACGCCTACCAGCGTACCTGGAAGCCGTTCAATCCAATTCTCGGTGAGACTTATGAGATGACTAATCATAATGGGAT
| | |||| || | | | | || ||| ||| || | | ||| | | | ||| | ||||| | || || ||| ||| || || | || |||||||| |||||||| |||||||| ||||||||||| |||
gtaagtatcaacatgctgtgtcttgcaataattttttcttacttctgtcaggctgttttatttcatcatttttcgtgtaagtgcagttcataagcacttcgctggagtaataatgaggttcttgtttgtgcagGCA-CTTGGGCAGTGTCAGTTTATCCCGCATATCAAAGGACATGGAAGCCTTTCAATCCTATTCTCGGGGAGACTTATGAAATG-----------------
upper sequence: AT5G02100.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S20_97V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaagcacatccccactcttcttgttcttccttgtagt---------tttttcatggtgtgac--------------taatttcatctgatctttaatagCATCATGGGCTATATCTGTGTATTACGCCTACCAGCGTACCTGGAAGCCGTTCAATCCAATTCTCGGTGAGACTTATGAGATGACTAATCATAATGGGAT
| | | || ||||| | | ||||| |||| || | ||| | | | | || || || ||| ||||||| |||| ||||| | ||| || ||| ||||||||||| |||||||| |||||||||||||| ||||||||| | | ||||| |
atcacttcgtcagtgtatctcttgcttatgtttgtaaggaagtaccgttttacaagcagtggcggctactgttcttacactattgtcgcctcatttgcagCTACATGGGCAGTATCGGTGTACTTCGCATATGCGCGGACCTGGAAGCCTTTCAATCCCATTCTCGGTGAGACCTATGAGATGGTCGACAAGAATGGCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttcttccttgtagttttttcatggtgtgactaatttcatctgatctttaatagCATCATGGGCTATATCTGTGTATTACGCCTACCAGCGTACCTGGAAGCCGTTCAATCCAATTCTCGGTGAGACTTATGAGATGACTAATCATAATGGGAT
tcttt CT-rich tract
atctttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcacatccccactcttcttgttcttccttgtagttttttcatggtgtgactaatttcatctgatctttaatagCATCATGGGCTATATCTGTGTATTACGCCTACCAGCGTACCTGGAAGCCGTTCAATCCAATTCTCGGTGAGACTTATGAGATGACTAATCATAATGGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG