Sequence
atgc intronic sequence ATGC exonic sequencegttggtctttatttctcattgtaaaagaactctcagatttcggattcttacatcactattgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G58560.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 8
gttggtctttatttctcattgtaaaagaactctcag-atttcggattcttaca---tcactattg--atccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
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gtcagatcataactctgtttgcagaat--tttacagtatttctaattttcatgaattgacaattgtaatcttctatgaaattctttca----gGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
gttggtctttatttctcattgtaaaagaactctcagatttcggattcttacatcactattgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
||| ||| || | || |||| | | || ||| || | || || | | |||| || || || ||||||| || | | || ||| ||||||| ||||||| ||||||||| ||||| ||| | || ||||||||||||||| || |||| |||
----gtccgtatgactacattcgctagtggtctctgttatctcattttttc--caggat--aacaataactatgttttttca--cagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G39210.1 (Glycine max), 3'ss of exon 7
gttggtctttatttctcattgtaaaagaactctcagatttcggattctta-catcactattgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
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gtaagtcgttcgctttgtttgttcat-attgaacagtgtgcttattttgaacatgacagtt-----ataaatttccccttctttttagGTGCACACTCTCTTGAAAGGATTGGAGAAAATTGCTGCCAGTGCAGACATTCCAATGTTGGTTTGTGGGGACTTTAATTCAATTCCAGGAAG
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA03G36550.1 (Glycine max), 3'ss of exon 7
gttggtctttatttctcattgtaaaagaactctcagatttcggattctta-catcactattgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
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gtaagtcgtttcttttgcttgttcat-attgaacagtgtgcttattttgaacatgacagtt-----ataaatttccccttctttttagGTGCACACTCTCTTGAAAGGATTGGAGAAAATTGCTGCAAGTGCAGATATTCCAATGTTGGTTTGTGGGGACTTTAATTCAATTCCAGGAAG
upper sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
------------------------gttggtctttattt---ctcattgtaaaagaactctcagatttcggattcttacatcactat-tgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
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gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAGMapped 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|116428969|gb|EG471561.1|EG471561EST: ACACGCATGTAAACGTTCCTCATGAATTGAAAGATGTAAAGCTGTGGCAG GTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATT
genomic: ACACGCATGTAAACGTTCCTCATGAATTGAAAGATGTAAAGCTGTGGCAGgttggtcttt ... gcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcagatttcggattcttacatcactattgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
ttcttgccc CT-rich tract
ataatgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttggtctttatttctcattgtaaaagaactctcagatttcggattcttacatcactattgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT