Sequence
atgc intronic sequence ATGC exonic sequencegtatacagttagttactttcgtgtgttgtgcaaaatattatttgttacaacggccttagagagttgctgactgagttcttcactccagGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTCAGGGATATCATGGTGTTGATAAGGAAGGAAGACCTGTTTACATCGAAAGATTAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G19650.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 3
--------------------------------gtatacagttagttactttcgtgtgttgtgcaaaatattatttgtt--acaacggccttagagagttgctgactgagttc-------ttcactccagGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTCAGGGATATCATGGTGTTGATAAGGAAGGAAGACCTGTTTACATCGAAAGATTAG
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gtgagttatccgatttgaaaaatataatcaacttattttggttgatcctgttttatttgatcaactgtactgtttttttgaaatcgttgttcatgctatactactttggtttcctgtctttctctttagGATTTTGAATTCGGTGAGTTGAATGAAGTCCTGCAGTACTATCCACATGGTTATCATGGTGTGGATAAGGAAGGAAGACCTGTTTATATTGAGAGGTTAG
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 3
----------------gtatacagttagttactttcgtgtgttgtgcaa-aatattatttgttacaacggccttagagagt------tgctg-actgagttcttcactcca--gGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTCAGGGATATCATGGTGTTGATAAGGAAGGAAGACCTGTTTACATCGAAAGATTAG
| | | | ||| ||| | || || || || || || ||| || | | | | | |||| | | | |||| | ||| ||||| || |||||| |||| || || | ||||||||| || || ||||||||||| |||| |||||||||||||||||| || || || |||
gtgatccatcttatacattaatatatgtttaatttgataatctgaacattgatttttttctttctttcggaatttggggttcatgtatattacactgtggtttctactctatagGATTTTGAATTCAAGGAGTTGAATGAAGTCCTGAAGTACTACCCGCATGGTTATCATGGTGTAGATAGGGAAGGAAGACCTGTTTATATTGAGAGGCTAG
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------gtatacagttagtt--actttcgtgtgttgtgcaaaatattatttgttaca-acggccttagagagttgctgactgagttcttcactccagGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTCAGGGATATCATGGTGTTGATAAGGAAGGAAGACCTGTTTACATCGAAAGATTAG
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gtgagtcatctgatttgaaaaatatatttcaacttcttattttggttgatcctgttttgtttgattaactgtacttttttagttttttgaaatcattgttcatgatatactactttggt---ttcctgtct------ttctctttagGATTTTGAATTCGGTGAGTTGAATGAAGTCCTGCAGTGCTATCCACATGGCTATCATGGTGTGGATAAGGAAGGAAGACCTATTTATATTGAGAGGTTAG
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S47_303V6.1 (Physcomitrella patens), 3'ss of exon 2
----------------------------gtatacagttagttactttcgtgtgttgtgcaaaatattatttgttacaacggccttagagagttgctgactgagttcttcactc---cagGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTCAGGGATATCATGGTGTTGATAAGGAAGGAAGACCTGTTTACATCGAAAGATTAG
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gttttggatcctggtgccatgatttagcatcttttgtaatttacttttaagattcctacacatgaacaaaatttacaggaatttgcggatactgaggctcctgttatgatgttgaacagGACTTCCAGTTCACCGAATTGGATTCAGTTCGAAAATACTATCCTCAAGGACACCATGGTGTTGACAAAGAAGGAAGACCTGTTTATATTGAGCAGATAGMapped 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|116424891|gb|EG467483.1|EG467483EST: CTAACATGATCCAATGGAGAAGGGATTTTGGCACAGACACAATCTTGGAG GACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTC
genomic: CTAACATGATCCAATGGAGAAGGGATTTTGGCACAGACACAATCTTGGAGgtatacagtt ... ttcactccagGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatattatttgttacaacggccttagagagttgctgactgagttcttcactccagGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTCAGGGATATCATGGTGTTGATAAGGAAGGAAGACCTGTTTACATCGAAAGATTAG
tgctgac putative branch site (score: 2)
ttcttcactcc putative PPT
tatttgtta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatacagttagttactttcgtgtgttgtgcaaaatattatttgttacaacggccttagagagttgctgactgagttcttcactccagGACTTTGAGTTTCCTGAGTTGGATGAGGTTCTCAGGTACTACCCTCAGGGATATCATGGTGTTGATAAGGAAGGAAGACCTGTTTACATCGAAAGATTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA