Sequence
atgc intronic sequence ATGC exonic sequencegttggttctttaattggaatatggttactctgttagttaaaaactacacttttgtcatatttttctgagattcattgatacatgttatgttttcagACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAACTGGAACCGCTGTTGAGTGGGTTCAGATGCCTGGAATGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G52150.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G52150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G01950.1 (Glycine max), 3'ss of exon 3
gttggttctttaattggaatatggttactctgttagttaaaaactacacttttgtcatatttttctgagattcattgatacatgttatgtttt------cagACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAACTGGAACCGCTGTTGAGTGGGTTCAGATGCCTGGAATGAAG
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--------gttagtgggactatcattattg-gctccctttctgtcacaacatggttctgtatttatgg--cttatggaatcatgtcttattctttttcccagGCTTTTGTCCATTGCAGAAGAGACTTTAGCAGAATTTCTTTCTAAGGCTACTGGAACTGCTGTTGAGTGGGTCCAAATGCCTGGAATGAAG
upper sequence: AT1G52150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G01940.1 (Glycine max), 3'ss of exon 3
gttggttctttaattggaatatggttactctgt-tagttaaaaact---acacttttgtcatatttttctgag--attcattgata-catgttatgttttc-agACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAACTGGAACCGCTGTTGAGTGGGTTCAGATGCCTGGAATGAAG
||| || || || ||| || | | | | || ||| || || || | || || || | | || | | |||| ||| | || |||||||||||||||||||| ||||||||||| |||||||| ||||| ||||| || |||||||||||||| || |||||||||||||||
gttagtgggagtatgattattgggtccctttctgtcactgtggtctgagacaacttggttatgtattcatggcttatgaaatcatgtcttattatttttcccagGCTTTTGTCCATTGCAGAAGAGACTTTAGCAGAATTTCTTTCTAAGGCTACTGGGACTGCTGTTGAGTGGGTCCAAATGCCTGGAATGAAG
upper sequence: AT1G52150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G21610.1 (Glycine max), 3'ss of exon 4
gttggttctttaattggaatatggttac-tctgttagttaaaaact---acacttttgtcatatttttctgagattcattgatacatgttatgtttt----cagACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAACTGGAACCGCTGTTGAGTGGGTTCAGATGCCTGGAATGAAG
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gttagtgggactatcattattggctcccattctttcactgtggtctgagacaacttggttgtgtattaatggcttatggaattatgtcttattctttttcccagGCTTTTGTCCATTGCAGAAGAGACTTTAGCAGAATTTCTTTCTAAGGCTACTGGGACTGCTGTTGAGTGGGTCCAAATGCCTGGAATGAAG
upper sequence: AT1G52150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G21620.2 (Glycine max), 3'ss of exon 3
gttggttctttaattggaatatggttactctgttagttaaaaactacacttttgtcata-tttttctgagattcattgatacatgttatgttttcagACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAACTGGAACCGCTGTTGAGTGGGTTCAGATGCCTGGAATGAAG
| || || | | ||| || | || ||||| | || | | | | || || | | | ||| |||||||||||||||||||| ||||||| ||| |||||||| ||||| ||||| || |||||||||||||| || |||||||||||||||
-------------------gttagtggaactatca-ttattggctccctttctgtcacaacttggttctgtattaatgtcttattctttttccccagGCTTTTGTCCATTGCAGAAGAGACTTTAGAAGAATTTCTTTCTAAGGCTACTGGGACTGCTGTTGAGTGGGTCCAAATGCCTGGAATGAAG
upper sequence: AT1G52150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g03740.t01 (Vitis vinifera), 3'ss of exon 3
gttggttctttaattggaatatggttactctgttagttaaaaactacac-ttttgtca-----tatttttctgagattcattgatacatgtta----tgttttcagACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAACTGGAACCGCTGTTGAGTGGGTTCAGATGCCTGGAATGAAG
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--------gttagtggggatatggttgttaggtccttttctgtcatcgtgctttgtgaccaccttgttgtgtgtggcttataagtttatgctaatattttttccagGCTTTTGTCCATTGCAGAAGAGACTTTAACAGAGTTTCTTTCAAAGGCCACTGGAACTGCTGTAGAGTGGGTCCAAATGCCTGGAATGAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|86068368|gb|DR364125.1|DR364125EST: CAGCACCAATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAGG ACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAAC
genomic: CAGCACCAATTGGCATCTCAAAATCCTCAGAGAGATGCTAGTCCTGCAGGgttggttctt ... atgttttcagACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactacacttttgtcatatttttctgagattcattgatacatgttatgttttcagACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAACTGGAACCGCTGTTGAGTGGGTTCAGATGCCTGGAATGAAG
cattgat putative branch site (score: 4)
tgttttc putative PPT
ttttgtcatattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggttctttaattggaatatggttactctgttagttaaaaactacacttttgtcatatttttctgagattcattgatacatgttatgttttcagACTTTTGTCCATTGCAGAAGAAACTTTAGCAGAGTTTCTTTCAAAGGCAACTGGAACCGCTGTTGAGTGGGTTCAGATGCCTGGAATGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG