Sequence
atgc intronic sequence ATGC exonic sequencegtgattttttctgtcaaccttgtctattttgttcttctgacttttatatgtcttacagtatgtaatctccttatgtgagagcaactgattggatgttgttttgtgaaacaataaatatatcatatggttggaatggctcttgtgcatgtgattgtctaattagatttgtgtatgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G52920.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 6
gtgattttttctgtcaaccttgtctattttgttcttctgacttttatatgtcttacagtatgtaatctccttatgtgagagcaactgattggatgttgttttgtgaaacaataaatatatcatatggttggaatggctcttgtgcatgtgattgtctaattagatttgtgtatgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG
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----------------------------------------------------------------gtttgttttgtttggagc--ttg--tggat-taagtttgtggaatg-tggagcccttgtttgct---gattgctgatgttga----actgtctactt----ttgc-catcctgtttagGCCATGGTTGCAAGAGGAGATCTTGGTGCAGAGCTCCCTATTGAAGAGGTTCCACTTTTGCAG
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 6
gtgatt-ttttctgtcaaccttgtctattttgttcttctgacttttatatgtcttacagtatgtaatctccttatgtgagagcaactga----ttggatgttg------ttttgtgaaacaataaatatatcatatggttggaatggctcttg--tgcatgtgattgtctaatta---gatttgtgtatgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG
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gtgctaatctaatcctcacgttatttactttatagttactgcctgattctggaaaatagggatgatttagcccatattataaaaacagaagcctttggtactgagtgtgttttgtttagagatcg-tggattaagtttttggggcacttgtttgctgattgttgatgttgaactgtctactttttccatcctgtttagGCCATGGTTGCAAGAGGAGATCTTGGTGCAGAACTCCCTATTGAAGAGGTTCCACTTTTGCAG
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 6
gtgattttttctgtcaaccttgtctattttgttcttctgacttttatatgtcttacagtatgtaatctccttatgtgagagcaactgattggatgttgttttgtgaaaca-ataaatatatcatatggttggaatggct--cttgtgcatgtgattgtctaattagatttgtgtatgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG
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----------------------------------------------------------------------------------tgcttcttaattcagatatcaaagaccttgcaactaggctttatgattgacctggacagttcatggatctaaatgctgaaaacattttgt---tcctctgtagGCAATGGTTGCTAGAGGGGATCTTGGTGCCGAGCTTCCTATTGAGGAGGTCCCATTGCTACAG
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ15169 (Selaginella moellendorffii), 3'ss of exon 4
gtgattttttctgtcaaccttgtctattttgttcttctgacttttatatgtcttacagtatgtaatctccttatgtgagagcaactgattggatgttgttttgtgaaacaataaatatatcatatggttggaatggctcttgtgcatgtgattgtctaattagatttgtgtatgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG
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--------------------------------------------------------------------------------------------------------------gtaagactaaggtttactttacgccgtttctgagaattatatcgcattctt----ttgcgtatc-----cagGCTATGGTTGCTAGAGGAGATCTTGGTGCCGAGCTTCCTATTGAAGACGTTCCCCTCCTTCAG
upper sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ08413 (Selaginella moellendorffii), 3'ss of exon 5
gtgattttttctgtcaaccttgtctattttgttcttctgacttttatatgtcttacagtatgtaatctccttatgtgagagcaactgattggatgttgttttgtgaaacaataaatatatcatatggttggaatggctcttgtgcatgtgattgtctaattagatttgtgtatgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG
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------------------------------------------------------------------------------------------------------------------gtaagac-taaggtttactttacgccgtttcttgaga--attatatcgcattcttttgcgtatc-cagGCTATGGTTGCTAGAGGAGATCTTGGTGCCGAGCTTCCTATTGAAGACGTGCCCCTCCTTCAGMapped 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|116479876|gb|EG522468.1|EG522468EST: GTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGG GCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTC
genomic: GTGCAGACTCCATACCTAACTTGCACTCCATTATCACAGCATCAGATGGGgtgatttttt ... tgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggaatggctcttgtgcatgtgattgtctaattagatttgtgtatgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG
gtctaat putative branch site (score: 3)
taattagattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgattttttctgtcaaccttgtctattttgttcttctgacttttatatgtcttacagtatgtaatctccttatgtgagagcaactgattggatgttgttttgtgaaacaataaatatatcatatggttggaatggctcttgtgcatgtgattgtctaattagatttgtgtatgtcttacagGCAATGGTTGCAAGAGGTGATCTTGGTGCAGAGCTTCCAATTGAAGAAGTCCCCATTCTTCAG
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