Sequence
atgc intronic sequence ATGC exonic sequencegtaaatccgacatatcttttatcatcaacaagggaaatagtttggatcttggttccgtatcaaatggattttggatttgcagATATGAGAAGGACATGCTTGCCTTTACAGGATGCAACCACAATCTTACAACTGAGGAAGCAGAAGAGCTGAGAATCATGAGGTACAGTGTCAAACATTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54100.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G399362_T01 (Zea mays), 3'ss of exon 6
gtaaatccgacatatcttttatcatcaacaagggaaatagtttggatcttggttccgt-atcaaatggattttggatttg--cagATATGAGAAGGACATGCTTGCCTTTACAGGATGCAACCACAATCTTACAACTGAGGAAGCAGAAGAGCTGAGAATCATGAGGTACAGTGTCAAACATTGG
||| | || | | | | | | | | | | | | ||| | | | || | ||| |||||| |||||||||||||| ||||| || || ||||||||||| || || || |||| ||||||| |||| ||| || || | |||
gtactggcctcaaactccggagcgttcagtacgtgatcggctggtcacgaggtcttttgaagagatcaccgcctgccttggacagATACGAGAAGGACATGCTGGCCTTCACCGGGTGCAACCACAACCTGACGCTGCGCGAGGCAGCGGAGCTGACGGGCATGCGGTTCAAGGTGCGGCGCTGG
upper sequence: AT3G54100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G020856_T01 (Zea mays), 3'ss of exon 6
------gtaaatccgacatatctttta-tcatcaacaag--ggaaatagtttggatcttggttccgtatcaaatggattttggatttg-cagATATGAGAAGGACATGCTTGCCTTTACAGGATGCAACCACAATCTTACAACTGAGGAAGCAGAAGAGCTGAGAATCATGAGGTACAGTGTCAAACATTGG
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gtagctgagagttcacagcgttcggtggccggctattatctgcagatcaatcaatggatgaacttgcattggtttgccttgatcgtcgtcagATACGAGAAGGACATGCTGGCCTTCACCGGGTGCAACCACAACCTGACGCTGGATGAGGCGGCGGAGCTGACGGACATGCGGTTCAAGGTGCGGCACTGG
upper sequence: AT3G54100.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g01650.t01 (Vitis vinifera), 3'ss of exon 6
-------------------gtaaatccgacat--atcttttatcatca-acaagggaaatagtttggatcttg-gttccgt---atcaaatggattttggatttgcagATATGAGAAGGACATGCTTGCCTTTACAGGATGCAACCACAATCTTACAACTGAGGAAGCAGAAGAGCTGAGAATCATGAGGTACAGTGTCAAACATTGG
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gtatgagaacttaatataactaaatacgtcatccacctaatatgagaacataagtgcattatcctttacggtgtgatccatctaattaaaccaatattga--tcacagATATGAGCAAGACATGCTTGCATTCACTGGATGCAGCCACAACCTTACCACAGAAGAGGCTGAGAAACTTAGAATTATGAGATACAGTGTCAAGCATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaagggaaatagtttggatcttggttccgtatcaaatggattttggatttgcagATATGAGAAGGACATGCTTGCCTTTACAGGATGCAACCACAATCTTACAACTGAGGAAGCAGAAGAGCTGAGAATCATGAGGTACAGTGTCAAACATTGG
aaatagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaatccgacatatcttttatcatcaacaagggaaatagtttggatcttggttccgtatcaaatggattttggatttgcagATATGAGAAGGACATGCTTGCCTTTACAGGATGCAACCACAATCTTACAACTGAGGAAGCAGAAGAGCTGAGAATCATGAGGTACAGTGTCAAACATTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA