Sequence
atgc intronic sequence ATGC exonic sequencegtatttttactcttttactcgatttgattgttttcgtttggtggtttagggatgtttctggaatcatgttgtggatttgtgattgaatcaatctgtttcgagtctggattaggttttctaggttttgctatgtatgacatttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaagGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G10480.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G10480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os01g50360.1 (Oryza sativa), 3'ss of exon 2
gtatttttactcttttactcgatttgattgttttcgtttggtggtttagggatgtttctggaatcatgttgtggatttgtgattgaatcaatctgtttcgagtctggattaggtt-ttctaggttttgctatgtatgacatttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaa---gGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAG
| ||| || || | || | | || |||| || ||| || ||| | |||| | |||| ||| || ||| || ||| | | |||| || || | || || ||| |||||||| || || ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || |
--------------------------------------------------------------------------------gtttggatt--tcgttaacggttttaccttcggttcttgtagcaattactaatagctagatttatag----cctgat-ttgccgtttttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAACAAGGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------
upper sequence: AT4G10480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g02960.1 (Oryza sativa), 3'ss of exon 1
gtatttttactcttttactcgatttgattgttttcgtttggtggtttagggatgtttctggaatcatgttgtggatttgtgattgaatca-atctgtttcgagtctggattaggttttctaggttttgctatgtatgacatttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaagGAGCTG---GTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAG
||| ||| ||||| ||| | || | || | || | || || ||| | | || ||| || | || ||| | | ||||| || || | || |||| |||||||| || || ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || |
-------------------------------------------------------------------------------------aatggtgtctctttcggttcttgtagcaattactaatgtactactctagatagcaagatttatagcct-gac-ttgcagttttaaatgaccttgaattgaagGTGAACAAGGTGCAATCGGAAACGAGGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------
upper sequence: AT4G10480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os07g22450.1 (Oryza sativa), 3'ss of exon 1
gtatttttactcttttactcgatttgattgttttcgtttggtggtttagggatgtttctggaatcatgttgtggatttgtgattgaatcaatctgtttcgagtctggattaggttttctaggttttgctatgtatgacatttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaa---gGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAG
|| ||| || | | || | || | || ||| || ||| | |||| | |||| ||| || ||| || ||| | | |||| || || | || ||| | | |||||||| || || ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || |
-------------------------------------------------------------------------------tgtttggatttcgttaacg-gtgttaccttcagttcttgtagcaattactaatagctagatttatag----cctgat-ttgcagtt-ttgatgaccttgaattgaagGTGAGCACGGTGCAGTTGTAAATAAAGGCTCCAAGCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGG---------
upper sequence: AT4G10480.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G171466_T01 (Zea mays), 3'ss of exon 1
gtatttttactcttttactcgatttgattgttttcgtttggtggtttagggatgtttctggaatcatgttgtggatttgtgattgaatcaatctgtttcgagtctggattaggttttctaggttttgctatgtatgacatttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaagGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAG
| | || |||| | | || || | || | | | | | ||| | || | | || || | || | | | | ||| | | | | ||| ||| || || | | |||| ||||||| || | ||||||||||| ||||| ||||| ||| |||| |||||||||||||| || || | || | |||
-----------------------------------------------------------------gtaacgacgacgtgtgtgttatctgttcccttctgcgttcag--cacgcagac--agatttaatttgcacg-----tgccagacgtggactgatttgagctgcggtgtc-tcgctctgggcgtgtagGCGCCGGCGCAACCGAGGGCACCAAGCAGAGCCGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACCGGCGTCACCAGMapped 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|124912383|gb|EH986463.1|EH986463EST: TGATGATGTTGATGACGACGACGATGAGATTGCTGATG GAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGC
genomic: TGATGATGTTGATGACGACGACGATGAGATTGCTGATGgtatttttac ... ttatgtgaagGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGC
EST:
gi|163995958|gb|ES206262.1|ES206262EST: ACGAAGACGATGATGATGTTGATGACGACGACGATGAGATTGCTGATG GAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCG
genomic: ACGAAGACGATGATGATGTTGATGACGACGACGATGAGATTGCTGATGgtatttttac ... ttatgtgaagGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaagGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAG
ttttgat putative branch site (score: 4)
ttgttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttttactcttttactcgatttgattgttttcgtttggtggtttagggatgtttctggaatcatgttgtggatttgtgattgaatcaatctgtttcgagtctggattaggttttctaggttttgctatgtatgacatttgttagggttttgatgttgttattgttgttgttgttgttgtttatgtgaagGAGCTGGTGAGAATGAGGCTTCCAAGCAAAGTAGAAGCGAGAAGAAAAGCCGAAAGGCGATGCTGAAACTCGGAATGAAACCTGTTACTGATGTTAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG