Sequence
atgc intronic sequence ATGC exonic sequencegtatgtaaagtgacactcataaaaagtgctttaataatacattttgtagagttattattcttaggatgtttggtctattttgcatatctgtctacgcaagatcagaaatctctatcaacaatataattggcttctcaatttgttttgctaatttgcccctggaatggtacagATGGGATTTCAATTTGCTGGGAAAGCATTGTATTCTGCTGTATGGGTTGCTGCTGTATCACTTTTCATGGAGTTGCTGGGTTTCTCTACACAAAAATGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10490.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA09G33170.1 (Glycine max), 3'ss of exon 8
gtatgtaaagtgacactcataaaaagtgctttaataatacattttgtagagttattattcttaggatgtttggtctattttgcatatctgtctacgcaagatcagaaatctctatcaacaatataattggcttctcaatttgttttgctaatttgcccctggaatggtacagATGGGATTTCAATTTGCTGGGAAAGCATTGTATTCTGCTGTATGGGTTGCTGCTGTATCACTTTTCATGGAGTTGCTGGGTTTCTCTACACAAAAATGGC
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-----------------------------------------------------gccaat-tgaagataattgtaaaaaattggattttggtgtatt---------gctttgttattagt--tatggttaaattc--aat--gacatagtaaattgtc--tgtcattgt-tagATGGGATTCCAATTTGCTGGCAAAGCTGTTTACTCTGCGGTATGGATAGCTGCCTTTTCACTGTTCATGGAATTGCTGGGCTTCTCTACCCAGAAATGGG
upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 8
gtatgtaaagtgacactcataaaaagtgctttaataatacattttgtagagttattattcttaggatgtttggtctattttgcatatctgtctacgcaagatcagaaatctctatcaacaatataattggcttctcaatttgttttgctaatttgcccctggaatggtacagATGGGATTTCAATTTGCTGGGAAAGCATTGTATTCTGCTGTATGGGTTGCTGCTGTATCACTTTTCATGGAGTTGCTGGGTTTCTCTACACAAAAATGGC
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--------------------------------------------attgaagatgataattgtaaaaaattggatttgg---gcgtattgttttgttattagttatggttcaatttcaatgacatagtaaatt-----gtctgtttttgt--------------------tagATGGGATTCCAATTTGCTGGCAAAGCTGTTTACTCTGCGGTATGGATAGCTGCCTTTTCACTGTTTATGGAATTGCTGGGCTTCTCTACCCAGAAATGGG
upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0313g00020.t01 (Vitis vinifera), 3'ss of exon 8
gtatgtaaagtgacactcataaaaagtgctttaataatacattttgtagagttattattcttaggatgtttggtctattttgcatatctgtctacgcaagatcagaaatctctatcaacaatataattggcttctcaatttgttttgctaatttgcccctggaatggtacagATGGGATTTCAATTTGCTGGGAAAGCATTGTATTCTGCTGTATGGGTTGCTGCTGTATCACTTTTCATGGAGTTGCTGGGTTTCTCTACACAAAAATGGC
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------------------------------------------------------tgatttttc---catttggactatcctgaaatgctgtctaatctcaa--ataaactgctagcttcaacaatcatggta---caatgaagttttctttcttgttg----------acagATGGGTTTCCAGTTTGCTGGAAAAGCTGTATACACTGCAGTATGGGTTGCTGCTGTTTCATTGTTCATGGAGTTGTTGGGTTTCTCTACCCAGAAATGGC
upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: PP1S79_156V6.1 (Physcomitrella patens), 3'ss of exon 7
gtatgtaaagtgacactcataaaaagtgctttaataatacattttgtagagttattattcttaggatgtttggtctattttgcatatctgtctacgcaagatcagaaatctctatcaacaatataattggc-ttctcaatttgttttgctaatttgcccctggaatggt-----------------acagATGGGATTTCAATTTGCTGGGAAAGCATTGTATTCTGCTGTATGGGTTGCTGCTGTATCACTTTTCATGGAGTTGCTGGGTTTCTCTACACAAAAATGGC
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---------gtaagacctattagaatggtttccgcgtctctctctttcttttccctatttatgcagtgt---gtttgtattacaagtggtcataggcagtatcctccgctcttttcgaactcgtaattgccattctagaacctttgcaggatgtggcctttggatttatttttgttcattccgtctgcagGTCGGTGTGCAATTCATTGGCAACACTGTATACACTGCTGTTTGGGTTGCTGCAGTGTGCCTTTTTATGGAGTTGTTGGGATTCTCGACGCAAAAATGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaatataattggcttctcaatttgttttgctaatttgcccctggaatggtacagATGGGATTTCAATTTGCTGGGAAAGCATTGTATTCTGCTGTATGGGTTGCTGCTGTATCACTTTTCATGGAGTTGCTGGGTTTCTCTACACAAAAATGGC
tgctaat putative branch site (score: 2)
aatttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtaaagtgacactcataaaaagtgctttaataatacattttgtagagttattattcttaggatgtttggtctattttgcatatctgtctacgcaagatcagaaatctctatcaacaatataattggcttctcaatttgttttgctaatttgcccctggaatggtacagATGGGATTTCAATTTGCTGGGAAAGCATTGTATTCTGCTGTATGGGTTGCTGCTGTATCACTTTTCATGGAGTTGCTGGGTTTCTCTACACAAAAATGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA