Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttctcacaaatgcctcctgtttctcttgctccaaaactcttttctttgaagtggaagttaactatttctctccttttgcagATGATAATAAAGTCTTTAACTGCCCTCACAGCTCTGATTCTTGAAGCCTTCGGTGTGTACTGTGAAGGAGAGTTTAAATGGGGATGTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G38360.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os06g51100.2 (Oryza sativa), 3'ss of exon 6
gtatgtttctcacaaatgcctcctgtttctcttgctccaaaactcttttctttgaagtggaagttaactatttctctccttttg---cagATGATAATAAAGTCTTTAACTGCCCTCACAGCTCTGATTCTTGAAGCCTTCGGTGTGTACTGTGAAGGAGAGTTTAAATGGGGATGTGG
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gtacgtggctctt---tatttcctgttctttttaattttcaagtgtctgatggaaattcaaactaatgcattctcttgttcctgggacagGTGATAATAAAGACAATTTGTGCTATTCTTGCGGTGATTCTTGAATCCTTTGGAGTGTACTGTGAAGGAGAGTTTAAGTGGAACTGTGG
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G088737_T01 (Zea mays), 3'ss of exon 5
gtatgtttctcacaaatgcctcctgtttctcttgctccaaaactcttttctttgaagtggaa-gttaactatttctctccttttgcagATGATAATAAAGTCTTTAACTGCCCTCACAGCTCTGATTCTTGAAGCCTTCGGTGTGTACTGTGAAGGAGAGTTTAAATGGGGATGTGG
|||||| ||| | || || | | ||| | | || || | || || | || | | ||| |||||||||||||| || || ||| | || ||||||||||| |||| || ||||||||||||||||||||||| | | |||||
gtatgtgcctc-----tatctt-tgatcacatggctttgcagcgtgttgtgaaaaatttgactaacaaattttctttgtcctttacagATGATAATAAAATCAATATGTGCTATTCTTGCGGTGATTCTTGAATCCTTTGGAGTGTACTGTGAAGGAGAGTTTAAGTTGAACTGTGG
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G373717_T01 (Zea mays), 3'ss of exon 4
gtatgtttctcacaaatgcctcctgtttctcttgctccaaaactcttttctttgaagtggaagttaactatttctct---ccttttgcagATGATAATAAAGTCTTTAACTGCCCTCACAGCTCTGATTCTTGAAGCCTTCGGTGTGTACTGTGAAGGAGAGTTTAAATGGGGATGTGG
|||||| ||| | || | | | ||| ||| | || | || | ||| | | |||| || |||| ||||||||||||||| || || ||| | || ||||||||||| |||| || ||||| ||||||||||||||||| | | |||||
gtatgtgcctctta----tctttcatcacaatggctttgcaaca-tgttgtgaaaattcgaactaactcattttccttgcccttgggcagATGATAATAAAATCAATATGTGCTATTCTTGCGGTGATTCTTGAATCCTTTGGAGTGTATTGTGAAGGAGAGTTTAAGTTGAACTGTGG
upper sequence: AT4G38360.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g03670.t01 (Vitis vinifera), 3'ss of exon 5
------------gtatgtttctcacaaatgcctcctgtttctcttgctccaaaactcttttctt------------tgaagtggaagttaactatttctctccttttgcagATGATAATAAAGTCTTTAACTGCCCTCACAGCTCTGATTCTTGAAGCCTTCGGTGTGTACTGTGAAGGAGAGTTTAAATGGGGATGTGG
||| | | | || || || |||| || | | ||||||| | | | ||| || ||||| | ||||||||||||||||||||||||| | ||| | |||| | ||||||||||||||| | |||| |||||||| || |||||||||||||||||
gtatgttttgtttcatggtgttggctcctgtttcttgcttcttttagctgttatccattttcttcttccttcacactaacaggaaagcaaattatttatactgttttgcagATGATAATAAAGTCTTTGAGTGCTATTTTAGCTGTAATTCTTGAAGCCTTCAGCTTGTATTGTGAAGGCGACTTTAAATGGGGATGTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctccaaaactcttttctttgaagtggaagttaactatttctctccttttgcagATGATAATAAAGTCTTTAACTGCCCTCACAGCTCTGATTCTTGAAGCCTTCGGTGTGTACTGTGAAGGAGAGTTTAAATGGGGATGTGG
agttaac putative branch site (score: 3)
ctatttctctcctttt CT-rich tract
ttaactattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttctcacaaatgcctcctgtttctcttgctccaaaactcttttctttgaagtggaagttaactatttctctccttttgcagATGATAATAAAGTCTTTAACTGCCCTCACAGCTCTGATTCTTGAAGCCTTCGGTGTGTACTGTGAAGGAGAGTTTAAATGGGGATGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA