Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G19880.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g67870.1 (Oryza sativa), 3'ss of exon 5
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattg-gctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
|| | | ||| || | ||||| | |||| | ||| || ||| | || | | | | ||||| || ||||||| |||||||| ||||| || || | ||||||||| || ||| ||||||||||||| |||||||| ||||| ||||| ||||||||||| | || |
--------------------------------------------------------------------------ttcagcagttaaatagta--tcatcttttgat-----ttttgtctatttaccaaccaagcatgatgagttgacagggtaatga-atttctactgatgcattgaaatagATTGGCGTTGAAAAGATGCATAAGGACAGCAAATATGTTTTGTTTCTGGATGATGATGTGAGACTGCACCCTGGGACAATTGGAGCTCTCACAAAAGAAA
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G061419_T01 (Zea mays), 3'ss of exon 5
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
| | | | | | | | | || | |||||| | | | || | | | | || | || ||||| | | | |||| || |||||||| |||||||| |||||||| ||||| || ||| | ||||||||||| || ||||||||||| || |||||||||||||| | || |
-----------------------------------------------------------------------tactgtggttactatatgttcatctcttggccttgttttattttttaccaaagaaggccagtaaattg-----actcgttactcatgtttat-----caaactgaaacagATCGGTGTTGAAAAGATGCACAAGGATACCAAGTATGTATTGTTTCTTGATGATGATGTGAGGCTGCATCCTGGGACTATCGGAGCTCTCACAAAAGAAA
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G35860.1 (Glycine max), 3'ss of exon 4
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaacc-atgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
||| |||||| | || || | | |||| | | | | | || ||| | | | | ||| | | | ||| | || ||||||| || | |||||| ||||||| ||||||||| ||||||||||||||||||||||| | ||||||||| |||||||||| ||||| |||||
----------------------------------------------------------------------------taacttatgaaattttggtccatttttattcttgttgatttcctagattgtccttgctagatgaattttaccaattacacttgtat-taacaccttg-----gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTATTTTTGGATGATGATGTTAGGTTACATCCTGGATCAATCGGAGCGCTCACTCGTGAGA
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G03760.1 (Glycine max), 3'ss of exon 5
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
| || ||||| | || ||| | | |||| | | | || | | ||| | | | | || | | | ||| | || ||||||| || | |||||| ||||||| ||||||||| || |||||||||||||||||||| || ||||||||| |||||||||| ||||| |||||
---------------------------------------------------------------------------ccgacattgaaattttggtccattttcattcttgttgatttcctagattgtctttgctagaggcattttaccaattacactagtat-taacaccttg-----gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAATATGTATTGTTTTTGGATGATGATGTTAGGCTACATCCTGGATCAATCGGAGCACTCACTCGTGAGA
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G01130.1 (Glycine max), 3'ss of exon 4
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
| | || | | | | || | || || || | | | |||| | | || | | | | |||| || | || ||||||| || |||||| ||||||| ||| ||||| |||||||| |||||||||||||| || ||||||||| |||| ||||| ||| ||| |
---------------------------------------------------------------------------gatgtctgggcaatttcattcctgttgatttgttaggttgtccttgct-tgatgcattttaccaactacactagtattacgtagtattggcacctgg-----gcagGTTGGAGTGGAGGCAATGCATAAAGATAGCAAGTATGTATTATTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGTGAAA
upper sequence: AT2G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G08510.1 (Glycine max), 3'ss of exon 4
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
| | | ||| | | | | || | || || || | | |||||| | || | | | | |||| || | || ||||||| || | |||||| ||||||| ||| ||||| || ||||| |||||||||||||| || ||||||||| |||| ||||| ||| || |
---------------------------------------------------------------------------aatgtctgggaaatttcattcctgttaatttgttaggttgtccttgct-tgattcattttaccaacgacactagtattacatagtattggcacctgg-----gcagGTTGGAGTGGAGACAATGCATAAAGATAGCAAGTATGTATTGTTTTTAGATGATGATGTTAGGCTACATCCTGGATCAATTGGAGCACTCGTTCGGGAAAMapped 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|164173459|gb|ES197758.1|ES197758EST: GGTTGCTTGGTTTATCAACAACATGTAGCCAGAAAATTCATAATCAGTTG ATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTAT
genomic: GGTTGC-TGGTTTATCAACAACATGTAGCCAGAAAATTCATAATCAGTTGgtatgtatga ... tttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
tgttcctgtttctggc CT-rich tract
ttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatgattttttttttctcccaatattttttttatctctcctttgtgactgttcttaaatcaactgtaatcacaaccatgaaaagctaacttatcttccaacatacatttttcatttttgttgttcattcattggctttcgctgaatgttcctgtttctggcttctttttcttgaagATTGGAGTTGAAAAAATGCACAAAGATACCAAATATGTGTTATTTTTGGATGATGATGTTAGACTGCATCCTGGAACAATCGGAGCTCTCACGACTGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT