Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgtttactgagtcatttgaggttcagagaattatgttttctggttggtttactgatttttggggttttatgtggtttttgatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTTGCTCGCCAGGTTGAGAAGGAGTTTAGGGAGTCTGCTCCGAGCTTGGATACT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G22330.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G080512_T01 (Zea mays), 3'ss of exon 2
gtttgtgtttactgagtcatttgaggttcagagaattatgttttctggttggtttactgatttttggggttttatgtggtttttgatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTTGCTCGCCAGGTTGAGAAGGAGTTTAGGGAGTCTGCTCCGAGCTTGGATACT---
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gttcgtttctctttca-catgtggaattcttttaatt-tatctaccagggagatagaatatattgtaataattgcatagtacgatgcatg-cagAAATGGCAGGAATCCTTTAGCCATAATCTTGGCACCAACAAGAGAACTTGCTCGGCAGGTTGAGAAGGAGTTTAGAGAATCTGCTCC---CTTGGACACCCTC
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G407382_T02 (Zea mays), 3'ss of exon 2
gtttgtgtttactgagtcatttgaggttcagagaattatgttttctggttggtttactgatttttggggttttatgtggtttttgatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTTGCTCGCCAGGTTGAGAAGGAGTTTAGGGAGTCTGCTCCGAGCTTGGATACT------------
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gttcgtttctctttca-catgtggaattcttttaatttatctaccagggagatataatatattgtaataatt-gcatagtacgaagcatg-cagatttggcagGAATCCTTTAGCCATAATCTTGGCACCAACAAGAGAACTTGCTCGGCAGGTTGAGAAGGAATTTAGAGAATCTGCTCC---CTTGGACACCCTCTGTGTATAT
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G407382_T01 (Zea mays), 3'ss of exon 2
gtttgtgtttactgagtcatttgaggttcagagaattatgttttctggttggtttactgatttttggggttttatgtggtttttgatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTTGCTCGCCAGGTTGAGAAGGAGTTTAGGGAGTCTGCTCCGAGCTTGGATACT---
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gttcgtttctctttca-catgtggaattcttttaatttatctaccagggagatataatatattgtaataatt-gcatagtacgaagcatg-cagATTTGGCAGGAATCCTTTAGCCATAATCTTGGCACCAACAAGAGAACTTGCTCGGCAGGTTGAGAAGGAATTTAGAGAATCTGCTCC---CTTGGACACCCTC
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------------------------------gtttgtgttt-actgagtcatt-----tgaggttcagagaattatgt---tttctggttggtttactgatttt-tggggttttatgtggtttttgatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTTGCTCGCCAGGTTGAGAAGGAGTTTAGGGAGTCTGCTCCGAGCTTGGATACT
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gttagttctattcttttttttaatgatatcgtgatgcttatgtttcgctatcacttgaatttgtaacttgtttctctgcgtgagttaaaggtggactaggcaattgctattggtgtggatgaaatcatggaaaatattgatttgttttttaactgtgcaagtttttttgtggtt---gatgtggcagGCGGGGGAGGGATCCTTTGGCTTTGGTTTTGGCTCCGACCAGAGAGCTTGCTCGACAGGTTGAAACGGAGTTCTGTGAGTCGGCACCTAATTTGGATACA
upper sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA08G41510.1 (Glycine max), 3'ss of exon 3
-------------------------------------------gtttgtgtttactgagtcatttgaggttcag-agaattatgtt-ttctggttggtttactgatttttggggttttatgtggtttttgatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTTGCTCGCCAGGTTGAGAAGGAGTTTAGGGAGTCTGCTCCGAGCTTGGATACT
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gtactttatatttggttacacttacatcttacttgaatctgtagccttgtttttctgcttgaagtaggattttctggtagtatatagtcttgatttgtgtctttaactaaacaaatttttgtggttgattattc---agGCAAGGAAGACATCCTTTGGCTTTGGTTTTGGCTCCGACTAGAGAACTTGCGCGGCAGGTTGAGAAGGAATTCAATGAGGCTGCACCTAACTTGGCCATGMapped 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|116406394|gb|EG448986.1|EG448986EST: TTTGGGATTCCTATCATTGACAAAATCATCAAATACAACGCTAAACATGG ACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTATG
genomic: TTTGGGATTCCTATCATTGACAAAATCATCAAATACAACGCTAAACATGGgtttgtgttt ... gatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCT-TG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttctggttggtttactgatttttggggttttatgtggtttttgatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTTGCTCGCCAGGTTGAGAAGGAGTTTAGGGAGTCTGCTCCGAGCTTGGATACT
tgattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgtttactgagtcatttgaggttcagagaattatgttttctggttggtttactgatttttggggttttatgtggtttttgatgtgatagACGAGGGAGGAATCCGCTTTGTTTGGTTTTGGCACCGACAAGAGAGCTTGCTCGCCAGGTTGAGAAGGAGTTTAGGGAGTCTGCTCCGAGCTTGGATACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT