Sequence
atgc intronic sequence ATGC exonic sequencegtatgctcgctcttctccagagaaaaatgcttcttccattaaccttagaaagattaaagttttctaattccactttacttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGCTTATTTGCATAATGGACGGCCCAATTCTTGATGAGAGTGGACATCTTATT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G37670.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G37670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g31690.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------------------------------------gtatgctcgctcttctccagag--aaaaatgcttcttccattaacct-tagaaagattaaagttttctaattccactttacttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGCTTATTTGCATAATGGACGGCCCAATTCTTGATGAGAGTGGACATCTTATT
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gtatgtttactgtattatttgaaattttgctgtgattaatgtgaatctgtgttcataattcttaagatatctaaaaatcagtatcatccatgtcatataccttatggagaatttcataagaaatagaagataattgcaccattttcctatagtaagtactgacataactattcttttgttacttt--cagCACATATGAAGTCGCTACAGCTTGTGCTTTAGCTATCGAGGCAGACAAGCTTATCTGCATTGTTGATGGTCAAATATTTGATGAACATGGTCGAGTCAAT
upper sequence: AT4G37670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G134426_T01 (Zea mays), 3'ss of exon 4
----------------gtatgctcgctcttctccagagaaaaatgcttcttccattaaccttagaaagattaaagttttctaattccactttacttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGCTTATTTGCATAATGGACGGCCCAATTCTTGATGAGAGTGGACATCTTATT
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taaagctctgaggaaaaaaaagatgcagtgttcgcaatagcatcacaggaccagttcgtatttatagggtctaacaagacttattttggcttatttt--cagTACCTATGAAGTTGCTACAGCATGTGCTTTATCCATAGAGGCGGACAAGCTTATTTGCATTGTTGATGGCCAAATATTTGATGAGCATGGTAGAGTCAAT
upper sequence: AT4G37670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G05060.1 (Glycine max), 3'ss of exon 4
------------------gtatgctcgctcttctccagagaaaaatgcttcttccattaaccttagaaagattaaagttttctaattccactttacttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGCTTATTTGCATAATGGACGGCCCAATTCTTGATGAGAGTGGACATCTTATT
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gctagacttgaataatgaatatggtgccctttctcccaaatgataagtctg----acaaatgcttggatcctggatattgatgagttatattttttttctccagCACCTATGAAGTTGCCACTGCTTGTGCCTTGGCTATAGGGGCAGACAAGCTAATATGCATAATAGATGGTCCAATACTTGATGAGAGTGGACACCTAATT
upper sequence: AT4G37670.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G17350.1 (Glycine max), 3'ss of exon 5
-gtatgctcgctcttctccagagaaaaatgcttcttccat-taaccttagaaagattaaagttttctaattcc--acttta-----------cttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGCTTATTTGCATAATGGACGGCCCAATTCTTGATGAGAGTGGACATCTTATT
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tttattttt-ctcttgaatgttgctatatagtacttggatgtgatccaacagaggcaaaaatgcttaaatactggattttgatgagttttgttttccacagTGCCTATGAAGTTGCGACAGCTTGTGCCTTGGCTGTACGAGCTGACAAGCTTATATGCATTACAGATGGTCCAATACTGGATGAAAGTGGACACCTTATTMapped 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|125325572|gb|EL339652.1|EL339652EST: GAGGAACTTGGGCCACTCGAGCTCCGGAGAAGTTCTTAAAATTGCAA TACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGC
genomic: GAGGAACTTGGGCCACTCGAGCTCCGGAGAAG-TCTT-AAATTGCAAgtatgctcgc ... acttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGC
EST:
gi|125064018|gb|EL131791.1|EL131791EST: TTGTTGAGGAACTTGGGCCACTCGAGCTCCGGAGAAGTCTTAAATTGCAA TACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGA
genomic: TTGTTGAGGAACTTGGGCCACTCGAGCTCCGGAGAAGTCTTAAATTGCAAgtatgctcgc ... acttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttccattaaccttagaaagattaaagttttctaattccactttacttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGCTTATTTGCATAATGGACGGCCCAATTCTTGATGAGAGTGGACATCTTATT
ttctaat putative branch site (score: 2)
ttccactttacttct CT-rich tract
aaagattaaagttttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctcgctcttctccagagaaaaatgcttcttccattaaccttagaaagattaaagttttctaattccactttacttctgcagTACCTATGAGGTTGCTACAGCTTGTGCTTTAGCTATAGGAGCAGATAAGCTTATTTGCATAATGGACGGCCCAATTCTTGATGAGAGTGGACATCTTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA