Sequence
atgc intronic sequence ATGC exonic sequencegtatgtcttagttttctcctgttacctatctaattaggcccatttgctaaatcattgggctgctcatccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G58560.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 5
------gtatgtcttagtttt--ctcctgttacctatctaattaggcccatttgc-taa-atcattgggctgctcatccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
||| | ||||| | || | || | || ||||| | ||| || | | || |||||||||| || ||||||||||||||||| ||||| || ||||| || | | | || | ||| ||||| | ||| ||| | |||
gtatctcaatggcagggtttttgttatagtcttcaattttcttcataccattcgtataatattttctgaacttcaatgtaggttgagTTTAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCAGCTGCTCAAAGAAAAGTGGCTTTAACTCGATTGATTAAG
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G118467_T03 (Zea mays), 3'ss of exon 5
gtatgtcttagttttctcctgttacct-atctaattaggcccatttgctaaatcattgggct-gctcatccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
||| | | | ||| | || || | || | ||| ||| || ||| | ||||||||||||| ||||||||||||||||| || || |||||||| |||| | ||||||| | | ||||| | ||| ||| | ||
gtacagttacttctgagtttgtagttttggctggtttg---cacctatctaattcttgcacttgcttgtgtagGTTGAGTTCAATAAGGCTGCACAGTCTTTAACAGATGCTATTATTCCTGCTGCCCAGAAAAGAGTGGCTTTAAGTCGATTGATTAAA
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 5
--gtatgtcttagttttctcctgttaccta----tctaattaggcccatttgc---taaatcat--tgggct--gct-catccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
|| ||| ||||| | | | | || | || || ||| | | ||| || | | || ||||| |||||||| ||||||||||||||||| ||||| || ||||| |||| | || || || ||| | ||||| ||||| |||
gtcagtgccttctttttcctgcagtgtttgagagttgacttgatactatcagcatctaatgctttctggactttgttatatgcagGTCGAGTTCAATAAGGCTGCACAGTCTTTAACTGATGCAATTATTCCTGCCGCTCAAAAAAAGTTAGCTCTAAATCGTTTGGTTAAG
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 4
-gtatgtcttagttt--tctcctgttacctatctaattaggcccatttgctaaatcattgggctgct-catccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
| | || ||| | || | || | | || || | || | | ||| |||||||| || ||||||||||||||||||||||| ||||||| || || | |||||||||| ||| ||||||||| |||| |||
gttgggaattgatttggcatatggtagttcaattatgtttgtacacaaattagaatgatgtgtgcttgcatgcagGTTGAATTTAACAAGGCTGCACAGTCTTTGACGGAGGCTACAATTCCAACCACTCAGAAGAAAACTGCCTTGAATCGGCTGGTTAAG
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G26620.2 (Glycine max), 3'ss of exon 4
-gtatgtcttagttt--tctcctgttacctatctaattaggcccatttgctaaatcattgggctgct-catccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
| | || ||| | || | || | | || || | || | | ||| |||||||| || |||||||||||||| |||||||| ||||||| || || | |||||||||| ||| |||||||| ||| |||
gttgggaattgatttggcatatggtagttcaattatgtttgtacacaaattagaatgatgtgtgcttgcatgcagGTTGAATTTAACAAGGCTGCACAATCTTTGACAGAGGCTACAATTCCAACCACTCAGAAGAAAACTGCCTTGAATCGACCGGTTAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgttacctatctaattaggcccatttgctaaatcattgggctgctcatccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
tgctaaa putative branch site (score: 2)
ctcatcc putative PPT
tatctaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtcttagttttctcctgttacctatctaattaggcccatttgctaaatcattgggctgctcatccagGTTGAGTTCAACAAGGCTGCACAGTCTTTGACTGAGGCTATTATCCCTGTTTCCCAGAAGAAAAATGCTTTGAATCGGTTGGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA