Sequence
atgc intronic sequence ATGC exonic sequencegtatatgccattattgaataaacgagaagagaaagtggttttatacaatcaaaagtcaatactttattagatcgcatgcaactacaatgcattcttaattgacatttacagGGCAAAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGAAGCTCTTCGACGTAATGTTGAAGCAAATTCTGTTTCTGAGCGTTGTATC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G04670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G04670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G154574_T01 (Zea mays), 3'ss of exon 7
gtatatgccattattgaataaacgagaagagaaagtggttttatac---aatcaaaagtcaatacttt--attagatcgcatgcaactacaatgcattcttaat---tgacatttacagGGCAAAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGAAGCTCTTCGACGTAATGTTGAAGCAAATTCTGTTTCTGAGCGTTGTATC
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-----------------------------gtacattctctttagcccttggtcaaacacttctgattctgattttatcccctctaaaaagtat-tattcttaatatcttactcttgcagGGCTAATGCCAAGCTAGTTTATGCATGTGAGTGGAATCCACATGCTCTGGAGGCTCTTCGGCGCAATGTTAGTGACAACAGAGTGGAGGATCGATGTATT
upper sequence: AT4G04670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G39030.1 (Glycine max), 3'ss of exon 7
gtatatgccattattgaataaacgagaagagaaagtggttttatacaatcaaaagtcaatactttattagatcgcatgcaactacaatgcattcttaattgacatttacagGGCAAAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGAAGCTCTTCGACGTAATGTTGAAGCAAATTCTGTTTCTGAGCGTTGTATC
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--------taatatctaattatccagcattgcttgcttctgaggtttgttaatatttaataat--attaatctatatttgttcatattgt-ttttgcatgttcttgagcagAGCCCAGGCAAAGCTTGTATATGCTTGTGAGTGGAATCCCCATGCTGTAGAAGCACTCCAACATAATCTAGAAGCAAATTCTGTGGCTGACCGTTGTATC
upper sequence: AT4G04670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G01710.1 (Glycine max), 3'ss of exon 6
gtatatgccattattgaataaacgagaagagaaagtggttttatacaatcaaaagtcaatactttattagatcgcatgcaactacaatgcattcttaattgacatttacagGGCAAAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGAAGCTCTTCGACGTAATGTTGAAGCAAATTCTGTTTCTGAGCGTTGTATC------------------------------------
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-------------------------------------------------------------------------------------------------------------------------------gtatatgcttgtgagtgaaatccccatgctgtagaagCACTCCAACATAATCTACAAACAAATTTTGTGGCTGATCGTTGTATCATACTTGAAGTAGATAATCGAATTACAGCTCCCAAG
upper sequence: AT4G04670.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv10s0116g01770.t01 (Vitis vinifera), 3'ss of exon 5
gtatatgccattattgaataaacgagaagagaaagtggttttatacaatcaaaa--gtcaatactttattagatcgcatgcaactacaatgcattcttaattgacatttacagGGCAAAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGAAGCTCTTCGACGTAATGTTGAAGCAAATTCTGTTTCTGAGCGTTGTATC
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----atgcctttggttggtgatttaactcttatggtctacttgattgctcacttttgcctttcctttactggaatgatttttattg----atactgttgtttgac-----cagTGCCAAGGCAAAACTGGTCTATGCTTGTGAGTGGAATCCCCATGCTGTTGAGGCGCTACAACATAATCTTCTTGCCAATTCTGTGGCTGATCGATGTATTMapped 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|116474296|gb|EG516888.1|EG516888EST: GTGGACCTGTTTGCTGGAATTGGATATTTTGTTCTCCCATTTCTTGTGAG GGCATAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGA
genomic: GTGGACCTGTTTGCTGGAATTGGATATTTTGTTCTCCCATTTCTTGTGAGgtatatgcca ... acatttacagGGCAAAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatactttattagatcgcatgcaactacaatgcattcttaattgacatttacagGGCAAAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGAAGCTCTTCGACGTAATGTTGAAGCAAATTCTGTTTCTGAGCGTTGTATC
aattgac putative branch site (score: 3)
ttaattgacattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatgccattattgaataaacgagaagagaaagtggttttatacaatcaaaagtcaatactttattagatcgcatgcaactacaatgcattcttaattgacatttacagGGCAAAAGCAAAGCTAGTATATGCTTGTGAGTGGAATCCCCATGCTATTGAAGCTCTTCGACGTAATGTTGAAGCAAATTCTGTTTCTGAGCGTTGTATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA