Sequence
atgc intronic sequence ATGC exonic sequencegtatttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G15930.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 4
gtatttccagagatcttttcctttattc---ttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
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gtttgtgttaaaactgctgactagttttaggatataaacttattctgttgagtaatatgtgttctcttttgca-taatcatgatgcagGGAATGGGATTTTTAGCTGGCTTGCTACTTCTTTATATGAGTGAAGAAGATGCATTTTGGTTATTAGTTGCTTTGCTGAAGGGAGCTGTTCATGCGCCAA
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 4
gtatttccagagatcttttcctttattcttatttgcccaagatggtact--aattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
|| | | ||| || | | | || || ||||| || ||| | | | | || | || ||||||||||||| || |||| || || |||||||||||||||| || || |||||||||||||||||||| || || || || ||||||||||| | ||||
gtttgttttgagttcggtgacctattttttcagatagaaagatctctctggaataatattctattgtttacacaattcattttgcagGGAATGGGATTTTTAGCTGGGCTGCTGCTTCTTTATATGAGTGAGGAGGATGCATTCTGGTTATTAGTCGCGTTGCTAAAGGGAGCTGTCCATGCACCAA
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G07090.1 (Glycine max), 3'ss of exon 3
gtatttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
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gttttactcaggaacccatcacctttctgtgcttgttacaaa--gta----tttcataatattgatcattttaaaacta---cagGGGATGGGGTTTTTAGCGGGACTTTTGCTTCTTTATATGAGCGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 4
gtatttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
|| || | || | || | | ||| | | ||| || | || | | | | ||||| | ||||| ||||| || |||| || | ||||||||||||||||| || || |||||||| ||||| || || ||||| || |||||||| || || | ||||
gttttactcaggaccccatcaccttgctgtgcttgttacaaa--gta----tttcataatattgaccattttaaaactc---cagGGCATGGGATTTTTAGCGGGGCTTTTGCTTCTTTATATGAGTGAGGAGGATGCATTTTGGTTGTTGGTGGCATTGCTAAAAGGAGCCGTTCATGCTCCAA
upper sequence: AT5G15930.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0083g00540.t01 (Vitis vinifera), 3'ss of exon 4
----gtatttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
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gtttggatctc-atgtatctcatcactcttctatttactgtttgtaggatactgaatgacattggat--tggtatcgtttgaaatgcagGGAATGGGATTTTTAGCTGGCTTACTGCTTCTTTATATGAGTGAAGAAGATGCATTCTGGTTGATGGTTGCATTACTTAAAGGAGCTGTTCATGCTCCAAMapped 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|124858117|gb|EH942554.1|EH942554EST: ATGTTCTAAAAGCATACTCTGTCTATGACAGAGATGTCGGATATGTTCAG GGAATGGGTTTCATAGC
genomic: ATGTTCTAAAAGCATACTCTGTCTATGACAGAGATGTCGGATATGTTCAGgtatttccag ... aataatgcagGGAATGGGTTTCATAGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
tactaaa putative branch site (score: 1)
tactaaaaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttccagagatcttttcctttattcttatttgcccaagatggtactaattacgaaagactcatggtactaaaaataatgcagGGAATGGGTTTCATAGCCGGTTTGTTGCTTCTTTATATGAGCGAAGAAGATGCATTCTGGTTATTAGTTGCATTACTCAAAGGAGCTGTCCACTCCCCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT