Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcttctttgctttttaatcttctttcttagtgatttgattactatgttgttggtttgttttgttgctcattggtttctgctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGCCTGCTATACTTGTCACTCCTCTAGGTGCTGTCAGTATCATTATCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71900.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g09140.2 (Oryza sativa), 3'ss of exon 2
----gtgagtcttctttgctttttaatcttctttcttagtgatttgattactatgttgttgg-tttgttttgttgc-tcattggtttctgctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGCCTGCTATACTTGTCACTCCTCTAGGTGCTGTCAGTATCATTATCAG
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tctaatatactgaagttactgtttcatttgtttttagacaaaaaatgtcactaaggaaagaaacttgactaatggcatcttacatgacctttgtgaacagTGATTGTGGGAGAAATTGCAAATTTTGCTGCTTATGCATTTGCTCCTGCTATTCTTGTTACTCCTCTTGGGGCACTCAGTATAATCATCAG
upper sequence: AT1G71900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G129268_T01 (Zea mays), 3'ss of exon 2
---------gtgagtcttctttgctttttaatcttctttcttagtgatttgattactatgttgttggtttgttttgttgctcattggtttctgctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGCCTGCTATACTTGTCACTCCTCTAGGTGCTGTCAGTATCATTATCAG
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tgcacagaactgctgctacaaccttttttaggagaacatgttactgaagctttctgaatgaaagaaacttgaaatat-gtacgt--acatgtgttttgtacagTGATTGTAGGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCTGCTATTCTTGTCACTCCTCTTGGTGCACTCAGTATAATCATCAG
upper sequence: AT1G71900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104147_T02 (Zea mays), 3'ss of exon 2
gtgagtcttctttgctttttaatcttctttcttagtgatttgattactatgttgttggtttgttttgt-tgctcattggtttctgctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGCCTGCTATACTTGTCACTCCTCTAGGTGCTGTCAGTATCATTATCAG
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----tgctactatcttttctaggagtacctgttactcaagctttctgaatgagagaaacttgaaatgtgttcacttacatgtcttttgtgcacagtgattgtagGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCAGCTATTCTTGTCACTCCTCTTGGTGCACTAAGTATAATCATAAG
upper sequence: AT1G71900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G104147_T03 (Zea mays), 3'ss of exon 2
-----gtgagtcttctttgctttttaatcttctttcttagtgatttgattactatgttgttggtttgttttgt-tgctcattggtttctgctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGCCTGCTATACTTGTCACTCCTCTAGGTGCTGTCAGTATCATTATCAG
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caaaactgctgctactatcttttctaggagtacctgttactcaagctttctgaatgagagaaacttgaaatgtgttcacttacatgtcttttgtgcacagTGATTGTAGGTGAAATTGCTAATTTTGCTGCTTATGCATTCGCTCCAGCTATTCTTGTCACTCCTCTTGGTGCACTAAGTATAATCATAAGMapped 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|125285141|gb|EL299226.1|EL299226EST: TGGGTATTCTTATCTCTACGAGCCTCTTTGGTGGATTGGCATGACGACAA TGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGC
genomic: TGGGTATTCTTATCTCTACGAGCCTCTTTGGTGGATTGGCATGACGACAAgtgagtcttc ... ctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgattactatgttgttggtttgttttgttgctcattggtttctgctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGCCTGCTATACTTGTCACTCCTCTAGGTGCTGTCAGTATCATTATCAG
atttgat putative branch site (score: 5)
tttctgctacttcc putative PPT
tttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcttctttgctttttaatcttctttcttagtgatttgattactatgttgttggtttgttttgttgctcattggtttctgctacttccagTGTTACTTGGTGAAATTGCCAATTTCGCTGCTTATGCATTTGCGCCTGCTATACTTGTCACTCCTCTAGGTGCTGTCAGTATCATTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC