Sequence
atgc intronic sequence ATGC exonic sequencegtattgaacactgagcgtttatttactctacagcatatatatttgtcgaatttcatcttacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25800.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 3
---------------gtattgaac--actgag-cgtttatt-----tactctacagcatatata-tttgtcgaatttcatcttacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
||||| | || | | |||| | | ||| |||| || ||| | || || || | |||| || ||||||||||||| || | || ||||| ||||| || |||||||||||||||||||||||||| || || |||||||| ||| || ||||| || |||||
ggagcaaatagtgcatgattgagccagttgggacatttactatacatgttctgcagcctaaataatgcatctaacaatattgctggccttttat-taccagATCAAGATTCCGTACGCTTGTTGGCAGTTGAAGGCTGTGCTGCTCTTGGGAAATTGTTGGAACCACAAGATTGTGTAGCACATATCCTTCCAGTTATTGT
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G102858_T01 (Zea mays), 3'ss of exon 3
------------------gtattgaacactgagcgtttatttact-ctacagcatatat---atttgtcgaatttcatct-tacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
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ttgtttgaatgttacaaggcatcagttatttgaaattagttcacagtcaaatcatacattacatcagctaagaagaaactgttttgactctttaactcagACCAAGATTCAGTGCGACTATTGGCAGTTGAGGGTTGTGCTGCTCTTGGGAAGTTGTTGGAGCCCCAAGATTGTGCAGCACATATTCTCCCAGTTATTGT
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 3
-------gtattgaa-cactgagcgtttatttactctacagcatatatatttg---------tcgaatttcatctt--acgtt----tttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
||||||| || |||| | ||| | |||| | |||| | | | ||| |||| | ||| | |||||||||||||| || | || ||||| ||||| ||||||||||||||||| |||||||||||||| || |||||||| ||||||||||| || |||||
ctaatcattattgaatcattgagttagtgtttgcatatagtcatacacttttgggacatcattagggctatgtctaaaacgtcgtggtctttattttcagATCAAGATTCAGTGCGTTTGTTGGCTGTTGAAGGTTGTGCTGCTCTTGGTAAATTGTTGGAGCCACAAGATTGTGTAGCTCACATTCTTCCAGTCATTGT
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G10790.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtattgaacactgag-cgtttatttactctacagcatatatatttgtcgaattt-catcttacgtttttttcata--tcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
| | | || | | | || | | | | ||| | ||| | | | | | || ||| ||||| | | ||||||||||| ||||||||||| ||||| || |||||||||||||||||||||||| || ||||||| || ||||| || ||| || || || || |||||
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaataca-attggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCGGTTATTGT
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G10790.2 (Glycine max), 3'ss of exon 3
------------------------------------------gtattgaacactgag-cgtttatttactctacagcatatatatttgtcgaat-ttcatcttacgtttttttcata--tcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
| | | || | | | || | | | | ||| | ||| | | | | | || ||| ||||| | | ||||||||||| ||||||||||| ||||| || |||||||||||||||||||||||| || ||||||| || ||||| || ||| || || ||
gtaattgaatacatatttctcattctttcttgatgtcttggcctgtcaatcataaattcaataataaattttccttaataca-attggcctagtatgcaatttaactttttaacctggctcagATCAAGACTCTGTTAGATTGTTGGCTGTGGAGGGTTGTGCTGCTCTTGGGAAACTGCTGGAGCCACAAGATTGCATCACACATATACTACCG--------
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 3
---------------------------------------------------------------gtattgaacactgagcgtttatttactctacagcat-------atatatttgtcgaatttcatcttacgtttt--tttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
|||| | || || || | || | || || || || || || ||| | | ||| | | | | |||||||||||||||| ||||| ||||| || ||||| |||||||||||||| || |||||||||| || |||||||| ||| || || || || |||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttttgtctattgcatattta-cattggttgtgtgattgtgttgtagaatctcctgaatgtactt-tcctcttttaatatgtgttgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGT
upper sequence: AT3G25800.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G24790.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------gtattga-acac-tgagcgt-ttatttactctacagcatatatatttgtcgaatttcatcttacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
|||| | | ||| || || | | ||| | | || || || || | || | | | | | |||||||||||||||| ||||| ||||| || ||||| |||||||||||||| || |||||||||| || |||||||| ||| || || || || |||||
gtaattgaatacatatttcttgttctttgtagatggaaagtgtctgtcatttgtctgttacatatttacatgtgtgattgtgttgtagagtctcctgaatgtactttactcctttaatatgcaattgtaatcttggaacagATCAAGATTCTGTCAGATTGTTGGCTGTGGAGGGCTGTGCTGCTCTTGGCAAGCTGTTGGAGCCACAAGATTGTGTTGCACATATACTCCCGGTTATTGTMapped 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|86040357|gb|DR336112.1|DR336112EST: GCATTTGAAGACCGACGTTATGTCCATGTTTGAGGATCTTACTCAAGATG ATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGA
genomic: GCATTTGAAGACCGACGTTATGTCCATGTTTGAGGATCTTACTCAAGATGgtattgaaca ... ttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttactctacagcatatatatttgtcgaatttcatcttacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
atcttac putative branch site (score: 3)
tcttacgtttttttc CT-rich tract
tttttttcatatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgaacactgagcgtttatttactctacagcatatatatttgtcgaatttcatcttacgtttttttcatatcagATCAAGATTCTGTTAGATTATTGGCCGTTGAGGGTTGTGCTGCTCTTGGGAAATTGTTGGAGCCTCAGGATTGTGTCCAACACATTCTTCCCGTGATTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG