Sequence
atgc intronic sequence ATGC exonic sequencegtaacagaaagattctgccttcaatatctctctctcgggaagttttgagacaagatctaatgtttctaaccatgtgattatacacatttaaatttcagAGAAAGCAAGTTGACAAGATTATTGAGAGACTCTTTGGGAGGAAAAACAAAAACATGTGTAATTGCTACAGTTTCACCCTCTGTTCATTGCCTGGAAGAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G28620.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G28620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 6
gtaacagaaagattctgccttcaatatctctctctcggga----agttttgagacaagatctaatgtttctaaccatgtgattatacacattt----aaatttcagAGAAAGCAAGTTGACAAGATTATTGAGAGACTCTTTGGGAGGAAAAACAAAAACATGTGTAATTGCTACAGTTTCACCCTCTGTTCATTGCCTGGAAGAA
||| | || | |||| || | | | || | || ||||| | || || | || |||| | | ||| |||| |||| || ||||| || ||||| |||||||| || || |||||||| |||||||||||||| ||||||| ||| | || ||||| |||| ||| |||||||
gtatgaactgcataattagttcagtaaattattattggcatatgaggtttgattttgaacttagaaattgaggtgaggtaattaaaaagattgcctgaaatatcagGGATAGCAAATTAACAAGGTTATTGAGGGATTCCTTGGGAGGGAAAACAAAAACATGCATAATTGCCACAATATCGCCCTCCATTCACTGCTTGGAAGAG
upper sequence: AT2G28620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S315_14V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaacagaaagattctgccttcaatatctctctctcgggaagttttgagacaagatctaatgtttctaaccatgtgattatacacatttaaatttcagAGAAAGCAAGTTGACAAGATTATTGAGAGACTCTTTGGGAGGAAAAACAAAAACATGTGTAATTGCTACAGTTTCACCCTCTGTTCATTGCCTGGAAGAA
|| | ||| | ||| | | | || | || || | | | | | | | ||| | | | || ||| || ||||||||||||||| | | ||||| |||||||| ||||||||||| ||||| | || || || || || || ||||| || ||||| || |||
gtgat-gaatcctgtaattttcgacttgttgctgccataaaattgaattccctcgtgttgtttggatttgaacgtgcctcatgtctcctcttttgcagGGATAGCAAGTTGACAAGACTGCTTAGAGATTCTTTGGGTGGAAAAACAAAGACATGCATCATAGCCACTGTCTCCCCATCTGTCCACTGCCTTGACGAA
upper sequence: AT2G28620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S13_177V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------gtaacagaaagattctgccttcaatatctctctctcgggaa-gttttga----gacaagatctaat---gtttctaaccatgtgatta-tacacatttaaatttc----------agAGAAAGCAAGTTGACAAGATTATTGAGAGACTCTTTGGGAGGAAAAACAAAAACATGTGTAATTGCTACAGTTTCACCCTCTGTTCATTGCCTGGAAGAA
|| | | ||| | | | || || | | || |||| | |||| | ||| ||| | || || | | | | ||| ||||| |||||| |||||||||| || || || |||||||||||||| ||||| || || | ||||| || ||||| ||||| ||||||||||| ||||||
gtaatttgtcctctgttgtgactatttgctggagtgacaaattccttcccagttttgtgttgattataattgtttctatttctattttcaactgtatgcctaatgtttctcttgacttcgtatggatacagAGATAGCAAGCTGACAAGATTGTTAAGGGATTCTTTGGGAGGAAAGACAAAGACCTGCATTATTGCCACCGTTTCGCCCTCCGTTCATTGCCTTGAAGAA
upper sequence: AT2G28620.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S6_143V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaacagaaagattctgccttc----aatatctctctctcgggaagttttgagacaagatctaatgtttctaa--ccatgtgatt-atacacatttaa-atttcagAGAAAGCAAGTTGACAAGATTATTGAGAGACTCTTTGGGAGGAAAAACAAAAACATGTGTAATTGCTACAGTTTCACCCTCTGTTCATTGCCTGGAAGAA
||| | | | || || | | ||| ||| | || || | | || | || ||| | | ||||| | |||||| || ||| |||||||||| || || || || ||||||||||| |||||||| ||| ||||||| || || || ||||| |||| ||| || |||||
---gtagagcattcttaattgggaaaaacatttatgcctctagaa--tgaaggatgagctttcgtgatggctgttcctcacaattcactcttctttaatgtcacagAGATAGTAAGCTGACAAGATTGTTAAGGGATTCCTTGGGAGGAAAGACAAAAACGTGTATAATTGCCACCGTCTCGCCCTCAGTTCCTTGTCTCGAAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgagacaagatctaatgtttctaaccatgtgattatacacatttaaatttcagAGAAAGCAAGTTGACAAGATTATTGAGAGACTCTTTGGGAGGAAAAACAAAAACATGTGTAATTGCTACAGTTTCACCCTCTGTTCATTGCCTGGAAGAA
ttctaac putative branch site (score: 1)
tgattatacacattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacagaaagattctgccttcaatatctctctctcgggaagttttgagacaagatctaatgtttctaaccatgtgattatacacatttaaatttcagAGAAAGCAAGTTGACAAGATTATTGAGAGACTCTTTGGGAGGAAAAACAAAAACATGTGTAATTGCTACAGTTTCACCCTCTGTTCATTGCCTGGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA