Sequence
atgc intronic sequence ATGC exonic sequencegtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G40760.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 7
--------------gtgagagctgcatagctaagacag-aaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttt--tcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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aaaaatataggtatatttcatttgtactattttaacagtatattgcca-acaatatggcatgccatagtagctgcaatttataatcaatacaatcctgcagATTGTATTCAGGGAGGACTTTGGGACTGACGGGCGTGGTGGATATTTTGATCAATATGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G130230_T03 (Zea mays), 3'ss of exon 7
----gtgagagctg--catagctaagacagaaatagtcagactgtttgttatttagagtca----attcacattttcaaatgct--tttct----tgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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tattgtaacaattgactacagtttgaaatgagtcaaactgaacctaagataactgaaagtacagtatcaatgacatggcatgctaattactacactgcagATTGTATTCAGGGAAGACTTTGGTACTGAAGGGCGTGGAGGATATTTTGACCAATATGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------------------gtgagagctgcata--gctaagacagaaatagtcagactgtttgttatttagagt---caattcacattttcaaatgcttt-------tcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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gtaagatcctttcctaggtggttacagtattttttttatttctttataaatcatggttggctgttataagttgataacacatcttttgtcagtttgtctgaagaattaaataaaattgatgtcaaaaagctgtattttttcagtaattattgtgcctaacatatgttcttgcatgtaatgaatgaattctgcagATCGTATTTAAGGAGGACTTTGGAACTGAAGGACGTGGAGGATATTTTGATCAATATGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G24250.1 (Glycine max), 3'ss of exon 7
---------gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagag------tcaattcacatttt-caaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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cttaacaatattttgttgccttatctaattcaactactgcattaccgtatttgatatggcacacttttaaacttgagttttgctgtcaattctctgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAATATGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 7
----------gtgaga-gctgcatagctaagacag-aaatagtcagac-tgtttgttatttagagtcaattcacattttcaaatgctttt---cttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
|| | | | || | | | || || || | | | | || | || | |||| || |||| | |||||| |||||||| ||| |||||||||||||||| || || |||||||||||| | |||||
aatttggtctgtctgttattacctaattcatctactgcatgaccaaacatttatatgccatatcttaaacttgagtttttggctgtttttactttggcagATCGTTTTCAGAGAAAATTTTGGAACTGAAGGTCGAGGTGGATATTTTGACCAGTATGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 7
--------------gtgagagctgcatagctaagacagaa-atagtcagactgtttgttatttagagtcaattcacatttt--caaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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attaacaatcttttgtt-gccttatctaattcaactactgcattgccagagttgatatggcacaattttaaactagagtttggctgttaattctatgacagATAGTTTTCAGAGAGGATTTTGGAACTGATGGCCGTGGTGGATATTTTGACCAGTATGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 7
--------------------gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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ggttacctcaaaatgttgaagtctctgatcgttttctatttcaaaataagtaatatgccataaacttaagcatgtggctattattt----tttttctttggcagATTGTGTTCAGGGAGGATTTTGGAACTGAAGGTCGTGGTGGATATTTTGATGAATATGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S73_244V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcac-attttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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gttaaaatagatcaatgcagtctatacatctctatttcatagtttgagaaggtgttcggatgtggttaccctctgattattttctagt-ttcatcttgcagATTGTTTTCAAGGAGGACTTTGGAACTGAAGGACGAGGCGGCTACTTCGACGAATACGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ21593 (Selaginella moellendorffii), 3'ss of exon 6
gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttc-aaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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--------------------------------gtatgggtgacaatgacaaatcatcgctagtgttctaaatagcatacatgcagATTGTGTTCAAGGAGAATTTTGGAACTGATGGTCGCGGTGGCTACTTTGACGAATATGG
upper sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ23968 (Selaginella moellendorffii), 3'ss of exon 6
gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttc-aaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
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--------------------------------gtatgggtgacaatgacaaatcatcgctagtgttctaaatagcatacatgcagATTGTGTTCAGGGAGAATTTTGGAACTGATGGTCGCGGTGGCTACTTTGACGAATATGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
tgcttttctt CT-rich tract
tttgttattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagagctgcatagctaagacagaaatagtcagactgtttgttatttagagtcaattcacattttcaaatgcttttcttgcagATTGTTTTCAGGGAAGATTTTGGAACTGAAGGGCGTGGCGGATATTTTGACGAATATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG