Sequence
atgc intronic sequence ATGC exonic sequencegtaaagaaatcttgtgttaagctcttgattcaatctgtttcttggtgtgatatatatatatatatatatgtatgtatcttataaatcactgacttgtgtgttactggtttcttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATATGATTACTTTGGATTTAAAACTCTTGAGAGATCGTACCTCTTGAAAGTCC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21790.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 3
gtaaagaaatcttgtgttaagctcttgattcaatctgtttcttggtgtgatatatatatatat-atatatgtat-gtatct-tataaatcactgacttgtgtgttactggtttcttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATATGATTACTTTGGATTTAAAACTCTTGAGAGATCGTACCTCTTGAAAGTCC
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-------------------atttcttgtgtggatatatttcttcaggtgcttcaattttttattatatgtatattgtgccaatgtgacttgataatttctatatgatgcaccatttcagAATACCACCCGCTTGGACAGTGAGATAATTTATGACAGAGATTTTGACTATGACTACTTTGGTTTTAAGACCCTTGAGAGATCTTATCTGTTAAAAGTTG
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------gtaaagaaatcttgtgttaagctc-ttgattcaatctgtttcttggtgtgatata-tatatatat-atata-tgtatgtatcttataaatcactgacttgtgtgttact--------ggtttc--ttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATATGATTACTTTGGATTTAAAACTCTTGAGAGATCGTACCTCTTGAAAGTCC
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gtgagattctagttgctcctggcacatttctgacagagcatctgtgtagataatgccgatgtgtttctggcagttgaatttactgttgcattcctttttttattaaggttgtttatctcatacagtaaatctgttgtgcccttcactcaccttgatgtaaattggccctcatatcgctccaaatgctgttacatttcagAATGCTGCTCGCTTGGACAGTGAAATAATTTATGATAGGGATTTCGACTATGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTCTTGAAGCTTG
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
gtaaagaaatcttgtgttaagctcttg-attcaatctgtttcttggtgtgatatatatatatatatatatgtatgtatcttataaatcactgacttgtgtgttactggtttcttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATATGATTACTTTGGATTTAAAACTCTTGAGAGATCGTACCTCTTGAAAGTCC
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----acaaggct---gtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaat---tggccctcacatgactccaaatgatgttacatt-------tcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
upper sequence: AT2G21790.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ14283 (Selaginella moellendorffii), 3'ss of exon 3
gtaaagaaatcttgtgttaagctcttgattcaatctgtttcttggtgtgatatatatatatatatatatgtatgtatcttataaatcactgacttgtgtgttactggtttcttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATATGATTACTTTGGATTTAAAACTCTTGAGAGATCGTACCTCTTGAAAGTCC
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-------------------------------------------------gtgagtattcccgtcattggttctccttttctgttctcatcagtttctctttctctt-ttcgtccagAACGCGGCGAAGCTTGATAGCGAAATCATCTATGACAGGGATTTCGACTATGACTACTTTGGATTCAAGACGCTCGAAAGATCATACCTCTTGAAAGTGAMapped 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|116415267|gb|EG457859.1|EG457859EST: GACTAAAGTCCCCACTAATAGCCGATGATGTGTTTGAGATAATTATGCAG AACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATAT
genomic: GACTAAAGTCCCCACTAATAGCCGATGATGTGTTTGAGATAATTATGCAGgtaaagaaat ... gtttcttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatatatgtatgtatcttataaatcactgacttgtgtgttactggtttcttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATATGATTACTTTGGATTTAAAACTCTTGAGAGATCGTACCTCTTGAAAGTCC
cactgac putative branch site (score: 2)
tttcttc putative PPT
tatgtatcttataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagaaatcttgtgttaagctcttgattcaatctgtttcttggtgtgatatatatatatatatatatgtatgtatcttataaatcactgacttgtgtgttactggtttcttcagAACGCTGCTCGTTTGGACAGTGAGATCATCTATGACCGTGATTTTGAATATGATTACTTTGGATTTAAAACTCTTGAGAGATCGTACCTCTTGAAAGTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC