Sequence
atgc intronic sequence ATGC exonic sequencegtatattttgacaaaagattgtgcaaatacctcatcgagtctttcactacctaaattgtttcctgggattatcaaaattttcttgcaatttataattttccagctgacagctaaggtttcatgaaaacatgaatgctttatttggattgtggctgcttttctgttttttattgggttatgtgtttatttctacagGTCGCGTGACACCTGAAAGTGTAATATACAGCTTTGGAACTCTATTACTTGACCTTCTGAGTGGAAAGCATATACCTCCAAGCCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G41260.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 6
gtatattttgacaaaagattgtgcaaatacctcatcgagtctttcactacctaaattgtttcctgggattatcaaaattttcttgcaatttataattttccagctgacagctaaggtttcatgaaaacatgaatgctttatttggattgtggctgcttttctgttttttattgggttatgtgtttatttctacagGTCGCGTGACACCTGAAAGTGTAATATACAGCTTTGGAACTCTATTACTTGACCTTCTGAGTGGAAAGCATATACCTCCAAGCCAT
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---------------------------------------------------------------------------------------------tattttgttatagattgtacaagat-cattagattatctttgtattaacatcaaagttctcaacatcgcattcctgcaaatgtcttttgttt-tacatgcagGACGTATTACTCCTGAAAGTGTCATATACAGCTTTGGAACCTTGCTGATTGATGTTCTTAGTGGGAAGCATATTCCTCCGAGCCAT
upper sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 7
gtatattttgacaaaagattgtgcaaatacctcatcgagtctttcactacctaaattgtttcctgggattatcaaaattttcttgcaatttataattttccagctgacagctaaggtttcatgaaaacatgaatgctttatttggattgtggctgcttttctgttttttattgggttatgtgtttatttctacagGTCGCGTGACACCTGAAAGTGTAATATACAGCTTTGGAACTCTATTACTTGACCTTCTGAGTGGAAAGCATATACCTCCAAGCCAT
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--------------------------------------------------------------------------tggtttaattatg-ttgcttattttatatcatataatctca-tatcataattatacgtata---tgatggcattgtgtctgccctccttttccctt----gccatg------------cagGCAGAGTTACTCCAGAGAGTGTAACATATAGCTTTGGGACCCTTTTGCTTGACCTCCTCAGTGGCAAGCATATTCCTCCAAGCCAT
upper sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G01730.2 (Glycine max), 3'ss of exon 6
gtatattttgacaaaagattgtgcaaatacctcatcgagtctttcactacctaaattgtttcctgggattatcaaaattttcttgc--aatttataattttccagctgacagctaaggtttcatgaaaacatgaatgctttatttggattgtggctgcttttctgttttttattgggttatgtgtttatttctacagGTCGCGTGACACCTGAAAGTGTAATATACAGCTTTGGAACTCTATTACTTGACCTTCTGAGTGGAAAGCATATACCTCCAAGCCAT
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---------------------------------------------------------------------tggcttaattatgttacttattttatatcctataatctcataccataa---ttataagtatatgatggc---------attgcgtctgccctccttttccct----ggccatg------------cagGCAGAGTTACTCCAGAGAGTGTAACTTATAGCTTTGGAACCCTTTTGCTTGACCTCCTCAGTGGCAAGCATATTCCTCCAAGCCGT
upper sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 7
gtatattttgacaaaagattgtgcaaatacctcatcgagtctttcactacctaaattgtttcctgggattatcaaaattttcttgcaatttataattttccagctgacagctaaggtttcatgaaaacatgaatgctttatttggattgtggctgcttttctgttttttattgggttatgtgtttatttctacagGTCGCGTGACACCTGAAAGTGTAATATACAGCTTTGGAACTCTATTACTTGACCTTCTGAGTGGAAAGCATATACCTCCAAGCCAT
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-------------------------------------------------------------------------------------------gcaatgcatacaatgcaatcttgtattttgagatgtaatgatttttttttgttggttact-ttgagttccgaaat---aatcggcattttctgcttttctgcagGAAGGGTAACACCTGAAAGTGTAATGTATAGTTTTGGCACCCTTTTGCTTGACCTTCTCAGTGGAAAACATATTCCTCCAAGCCAT
upper sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S178_86V6.1 (Physcomitrella patens), 3'ss of exon 5
gtatattttgacaaaagattgtgcaaatacctcatcgagtctttcactacctaaattgtttcctggga-ttatcaaaattttcttgcaatttataattttccagctgac--agctaaggtttcatgaaaacatgaatgctttatttggattgtggctgctt-ttctgttttttattgggttatgtgtttatttctacagGTCGCGTGACACCTGAAAGTGTAATATACAGCTTTGGAACTCTATTACTTGACCTTCTGAGTGGAAAGCATATACCTCCAAGCCAT
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---------gtaccaacttggcatacacccccccatgagtacttaagaactggtaacgaagtctgaagcttggtaatgtatttgcgcaattctggacattattacggacctacccaaaattacc----aacattcaaagcagccctggatttagtatgcttactttggattcctgagattcttgtattcaaatttgcagGTAGGGTGACACCTGAAAGTGTTATTTACAGCTATGGAACTGTTCTACTAGATCTGTTGAGTGGGAAGCATCTACCTCCTAGTCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttggattgtggctgcttttctgttttttattgggttatgtgtttatttctacagGTCGCGTGACACCTGAAAGTGTAATATACAGCTTTGGAACTCTATTACTTGACCTTCTGAGTGGAAAGCATATACCTCCAAGCCAT
tttatttct CT-rich tract
ttttctgttttttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattttgacaaaagattgtgcaaatacctcatcgagtctttcactacctaaattgtttcctgggattatcaaaattttcttgcaatttataattttccagctgacagctaaggtttcatgaaaacatgaatgctttatttggattgtggctgcttttctgttttttattgggttatgtgtttatttctacagGTCGCGTGACACCTGAAAGTGTAATATACAGCTTTGGAACTCTATTACTTGACCTTCTGAGTGGAAAGCATATACCTCCAAGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA