Sequence
atgc intronic sequence ATGC exonic sequencegtatgttcatataatcatcatggagtaatgttgttttttggtacaagtttttgaaatttgtacttcttagGTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGACCTTAAGAAGCAACTAGAGGAAGCTAGGTCCAAGGGCATCTCTGTAAGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72330.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 8
---------gtatgttca-tataatcatcatggagtaatgttgttttttggtacaagttt--ttgaaatttgtacttcttagGTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGACCTTAAGAAGCAACTAGAGGAAGCTAGGTCCAAGGGCATCTCTGTAAGGG
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gtatgttttgaattctcagcacattttcaatatggctgcattcatgctgcaccaaagcctaattgagagcattttgttttagGTCCCGTATTATCTTAATGAATCAACAGGCTGGGGTTTGGAGATCTCTGACCTTAAGAAGCAACTCGAAGATTCTCGGTTGAAAGGCATTGATGTTAGGG
upper sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA16G01630.2 (Glycine max), 3'ss of exon 6
--------------------------gtatgttcatataat-catcatggagtaatg-ttgttttttggtacaagttt--ttgaaatttgtacttcttagGTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGACCTTAAGAAGCAACTAGAGGAAGCTAGGTCCAAGGGCATCTCTGTAAGGG
| || || | | ||| || ||||| || || || || || | ||| | | | |||| || || ||||| |||||||||||||| ||||| |||||||| |||| || ||||||||| | |||| || | ||| ||||||||| ||| ||||
tgtatatgtgcattattgacatgaaactttgaatatgaactatatcttgttataatgcttaggttggattatcagcttaactacaatattttttctaaagGTACCTTATTATCTAGATGAAGCAACAGGTTGGGGGTTGGAAATACCTGAACTCAAGAAGCAATTGGAGGCTGCCAAGTCTAAGGGCATCAATGTTAGGG
upper sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 8
---------------------------------gtatgttcatataatcatcatggagtaatgttgttttttggtacaagtttttgaaatttgtacttcttagGTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGACCTTAAGAAGCAACTAGAGGAAGCTAGGTCCAAGGGCATCTCTGTAAGGG
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tgggagagtgatcagagttacattatcctcaccgcatttgcacttttttcccaaagggcttgtatattcttaagaatataatctt---actttggttttgcagGTTCCTTACTATCTTGATGAAGCAACTGGGTGGGGCTTGGAGATTTCAGAACTTCAGAAGCAATTGGAAGATGCAAAGTCAAAGGGTATCACCGTTAGGGMapped 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|86054017|gb|DR349774.1|DR349774EST: CTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATGGTGGATCTTTG GTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGAC
genomic: CTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATGGTGGATCTTTGgtatgttcat ... tacttcttagGTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGAC
EST:
gi|86054013|gb|DR349770.1|DR349770EST: CTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATGGTGGATCTTTG GTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGAC
genomic: CTCAGTATCCATTGTACTCGGCTTCAATTGCCCTTCATGGTGGATCTTTGgtatgttcat ... tacttcttagGTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catcatggagtaatgttgttttttggtacaagtttttgaaatttgtacttcttagGTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGACCTTAAGAAGCAACTAGAGGAAGCTAGGTCCAAGGGCATCTCTGTAAGGG
tacttctt CT-rich tract
aagtttttgaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttcatataatcatcatggagtaatgttgttttttggtacaagtttttgaaatttgtacttcttagGTTCCGTACTATCTTGATGAAGCAACAGGATGGGGACTGGAAATATCTGACCTTAAGAAGCAACTAGAGGAAGCTAGGTCCAAGGGCATCTCTGTAAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA