Sequence
atgc intronic sequence ATGC exonic sequence...gaaaaaaacgaagttcaataaccagaacaagttaaaccgtaaaaagccaatgtccatgcttattccgattcatttatattttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52570.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G37560.2 (Glycine max), 3'ss of exon 2
gaaaaaaacgaagttcaataaccagaacaagttaaaccgtaaaaagccaatgtccatgcttattccgattcatttat--attttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG
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--------gtaagtcctatactcctatatctatttattatgaaat-tgggtatataattcaattctgcgtcttgaattcaattgggtatgtctaattttcagGTGGCTATGGAATTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G30230.2 (Glycine max), 3'ss of exon 2
gaaaaaaacgaagttcaataaccagaacaagttaaaccgtaaaaagccaatgtccatgcttattccgattcatttatattttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG
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--------gtaagtcctatatctttattatg--aaattg----ggtttattattcaattctgggt--gttgaatt-caattgggcatgtctaattttcagGTGGCTATGGAACTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGCTTCCTTGTGGCACATGCACGAG
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G29790.1 (Glycine max), 3'ss of exon 2
-------------------------gaaaaaaacgaagttc--aataaccagaacaagttaaaccgtaaaaagccaatgtccatgcttatt--ccgattcatttat--attttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG
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gtgagttatcctttaaactaattatgattccaattgggttttgaatggtttttgagttcagaattgggtgagttgtttgtgaattttgagtgttagattcaagtattcaactgggtatgtctgattttcagGTGGGTATGGAATTTTGGGCTAGATGGGCTCATAGGGCTCTCTGGCATGCTTCGCTGTGGCACATGCATGAG
upper sequence: AT5G52570.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G24530.1 (Glycine max), 3'ss of exon 2
-----------------------gaaaaaaacgaagttcaataaccaga-acaagttaaaccgtaaaaagccaatgtccatgcttattccgattcatttat--attttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG
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gtgagtaatcatccttttaattgattatgattccaattcagttttgaattgctttttaattcagaattgggtgagttctttgtgaattttgggtggtagattcaattgggtatgtctgattttcagGTGGGTATGGAGTTTTGGGCTAGATGGGCTCACAGGGCTCTATGGCATGCTTCCCTGTGGCACATGCATGAGMapped 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|86073437|gb|DR369194.1|DR369194EST: TGTCTGTGTTNNNNATGTTTGGCACATTTGCTCTTTCCGTTGGTGCTGCC GATGGGATGGAGCTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGAT
genomic: TGTCTGTGTTAGAGATGTTTGGTACATTTGCTCTTTCCGTTGGTGCTGCCgtaagtttca ... tgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gccaatgtccatgcttattccgattcatttatattttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG
attcatttatattttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaaaaaacgaagttcaataaccagaacaagttaaaccgtaaaaagccaatgtccatgcttattccgattcatttatattttcgtatatttgaattttagGTTGGGATGGAGTTTTGGGCAAGATGGGCTCATAGAGCTCTTTGGCATGATTCTTTATGGAACATGCATGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- aaaaaac
- - - - - - - -caataac
- - - - - - - - - - - cagaaca
- - - - - - - - - - - - - - - -ttaaacc
- - - - - - - - - - - - - - - - - - - - - -aagccaa