Sequence
atgc intronic sequence ATGC exonic sequencegtaattcttttttctgttatatcacctaaattttctttgaataaaactatgtaaccataattaaagatattcctccctctcttgggtctctgcctctctggtccataattgacaccccttattacttttctatttcttttgtgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G30450.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
gtaattcttttttctgttatatcacctaaattttctttgaataaaactatgtaaccataattaaagatattcctccctctcttgggtctctgcctctctggtccataattgacaccccttattacttttctatttcttttgtgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC
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----------------------------------------------------------------------------------------------aatgttggtaatacttt-tagagcttgctttgattttgttcattgc-tgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
gtaattcttttttctgttatatcacctaaattttctttgaataaaactatgtaaccataattaaagatattcctccctctcttgggtctctgcctctctggtccataattgacaccccttattacttttctatttcttttgtgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC
|| || | ||| || | |||| | || |||| || ||| | | |||||| ||| | | || | || | ||| || | | |||| || | ||||||| || |||||||| ||||||||||| || |||||||| |||||||| ||||||| || |||| || || ||||| |||||||| |||||| |||
----------------------------------------------------------------------------ctttcataactct-tgttttactggcttaggctt------ccttctt--tttgttgtcctttttgt-attaattgataccaa-----tctattttcttgacatcttt---gt--ttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ23975 (Selaginella moellendorffii), 3'ss of exon 3
gtaattcttttttctgttatatcacctaaattttctttgaataaaactatgtaaccataattaaagatattcctccctctcttgggtctctgcctctctggtccataattgacaccccttattacttttctatttcttttgtgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC
|| ||| || | || | || |||| ||| || |||| ||||||| ||||| ||||| || |||||||| ||||||||||||||||| || ||||| || || | |||||||| ||||| ||||| ||||||||| | |
----------------------------------------------------------------------------------------------------------------------------------------gttcaaaattttgcgttgcgacagtttttcttttggttaagcact---ggtttat---agGGTGGCGGACCGTATTATCTGATTGGTCGAGCTCTTGGTCCGGAAGTCGGTATTAGTATTGGGCTTTGCTTTTTCCTTGGAAATGCGGTTGCTGGATCAC
upper sequence: AT1G30450.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ21598 (Selaginella moellendorffii), 3'ss of exon 3
gtaattcttttttctgttatatcacctaaattttctttgaataaaactatgtaaccataattaaagatattcctccctctcttgggtctctgcctctctggtccataattgacaccccttattacttttctatttcttttgtgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC
|| | ||| || | || | || |||| ||| | |||| ||||||| ||||| ||||| || |||||||| ||||||||||||||||| || ||||| || || | |||||||| ||||| ||||| ||||||||| | |
----------------------------------------------------------------------------------------------------------------------------------------gttcgaaattttgcgttgcgacagtttttcttttggttaagcactgct---ttat---agGGTGGCGGACCGTATTATCTGATTGGTCGAGCTCTTGGTCCGGAAGTCGGTATTAGTATTGGGCTTTGCTTTTTCCTTGGAAATGCGGTTGCTGGATCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC
taataac putative branch site (score: 1)
ttatctc putative PPT
tatttaagacatcaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattcttttttctgttatatcacctaaattttctttgaataaaactatgtaaccataattaaagatattcctccctctcttgggtctctgcctctctggtccataattgacaccccttattacttttctatttcttttgtgattgaacggtatttaagacatcaagtttattaataacttttgggttatctcagGGTGGAGGACCATATTACCTCATTGGTCGCGCTCTTGGTCCGGAAGTTGGGATTAGCATAGGTTTATGCTTTTTTCTTGGCAATGCAGTTGCTGGAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT