Sequence
atgc intronic sequence ATGC exonic sequencegtaatgcttgatttctgctcctggagttctttttttttttcgttcttgtttgatggaagttgtaaaaggctgtactgattgaaataaaatttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55150.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
--gtaatgcttgatttctgctcctggagttctttttttt------tttcgttcttgtttgatggaagttgtaaaaggctgtactgattgaaataaaatttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT
| | | || || | || | |||| || || | ||| ||| ||| | | || | | | | || || ||| || | ||| || || ||||| || |||| | || || || |||||||| |||||||||||||||||||||||| |||| |||||| | || ||||||||
gtgcgaaatgttgcttatgtttcttaaccgattttcttggatacattctggacttcttttgtggtaatctactaacatttttccgtgtgttattaaa-------gCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 3
gtaatgcttgatttctgctcctggagttctttttttttttcgttcttgtttgatggaagttgtaaaaggctgt-actgattgaaataaaatt----tcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT
| || | || | | | | ||||| || | | |||| | ||| | | | || ||| || | ||| | ||| || || ||||| |||||||| | ||||| || |||||||| ||||| |||||||||||||| ||| | || |||||| |||| ||||| ||
-----gtgagaact-tgtttccccaatgcttttccttctcaaccatcttttgggaactccagctaaaaattctgaacacttacaattttgttgttgttgaagCCCCTGGCGATGGTCCAATTGTCTTGGTGTTAGCTCCTACACGTGAACTTGCTGTTCAGATACAGCAAGAAGCAACCAAGTTTGGTGCATCATCAAAGAT
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 3
--------gtaatgct-tgatttctgctcctggagttcttttt---ttttttcgttcttgtttgatggaagttgtaaaaggct--gtactgattgaaataaaat-ttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT
||| | | | | | || ||| | || | | || | | || | ||| | || ||| || || || ||| || ||| || || ||||| || || ||| | ||||| ||||||||||| ||||| || ||||| |||||||| ||||||||||| |||| || | ||
gtaaggaaataaggaaacaactgagacaattagatttcatattggatgtaagggtgccttttctgactatgttacctttgtcttgccgtccattcgtttacgatattttcagATCCTGGAGATGGACCAATTGTGTTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGGCTACTAAATTTGGTGCATCATCTAGGAT
upper sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------gtaatgcttgatttctgctcctggagttcttttttttttt-cgttcttgtttg-atggaagtt--------gtaaaaggctgtactgattgaaataaaatttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT
|||| |||||||| | | | | | | | | | | | | || | | || || | | | | | | || | | |||| |||||| || || |||||||| || || ||| | ||||| ||||||||||| ||||| |||||||| ||||| ||| ||||||||||| |||| || | ||
gtataagtgtctttctaattcgttgatgtcgctaatttctgatttctatctatctatctatctatctatatatatatatatatgcacacacatttttttctagttacaagttttggtc-tttctctgtattttctcagCTCCAGGAGATGGCCCAATTGTATTAGTTTTAGCTCCAACTCGTGAACTTGCTGTTCAGATACAACAAGAAGCAGCTAAATTTGGTGCATCATCGAGGATMapped 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|116454669|gb|EG497261.1|EG497261EST: TTCTTACTTACTACCTGCTATTGTCCATGTTAATGCCCAACCAATGTTAG CTCATGGTGACGGCCCAATCGTCTCGGTTCTTGCTCCCACTCGTGAACTGG
genomic: TTCTTACTTACTACCTGCTATTGTCCATGTTAATGCCCAACCAATGTTAGgtaatgcttg ... aatttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcttgtttgatggaagttgtaaaaggctgtactgattgaaataaaatttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT
tactgat putative branch site (score: 2)
tttccc putative PPT
tgattgaaataaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgcttgatttctgctcctggagttctttttttttttcgttcttgtttgatggaagttgtaaaaggctgtactgattgaaataaaatttcccagCTCATGGTGACGGCCCAATCGTCTTGGTTCTTGCTCCCACTCGTGAACTGGCTGTGCAGATACAGCAAGAGGCATCTAAATTTGGTTCATCCTCAAAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG