Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G14840.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 5
-----gtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
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gtattgcaatcttgtatgattattctctc-tcctggtgtgtgagaatcata-atatgtaacttctatctc--------tgactttgc---------catcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAGCTAGAAGAGGCTGTCCTTGCAG
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 5
gtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
|| | | || | | | |||| | |||| | || | || | | ||| | | | || || | | | ||||||| |||| |||| | ||||| ||||| ||||||||||| ||||| ||||||||||| | || | |||| | ||| ||||||| ||||| ||||| |
----gtat-tgcaatcttgtatgattattctctctccag----gtgtgtgagaaccataatatgtaacttctatcttcggactttgccatcaacttcct----cagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 5
gtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
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----gtatttgcaatttcgtatg-gtgtttccctctccaagtatgccagccttaataatgtaatttcttatatttggttttggtatcat--catcacctctcctagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG
upper sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 5
gtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
| | | | ||| | || | || | | || || | | | | | || | | ||| | || ||| | ||||||| |||| |||| | ||||| ||||| |||| |||||| ||||| ||||||||||||| || | || | ||| ||||||| ||||| ||||| |
--gtatttgcaat-tttgtattgtgt-ttctctctcaagtatgccagacataataatgtaatttctgacatt-tggtttcat---------catcacctctcccagGAAGAAAATAAAATTTTGGACAAAATGCATAGACTGAAGGTGGCAGAGGTTGAAAAGCTTACCCAAACCGTGAGAGAACTAGAAGAGGCTGTCCTTGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
ttaaaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT