Sequence
atgc intronic sequence ATGC exonic sequencegtacgagatatggtttcagctgtggtttcagagtagtagcatcttgctgtggaactaacaacattttacaaattgataaaatagGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G56160.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G56160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G48060.1 (Glycine max), 3'ss of exon 4
-----gtacgagatatggtttcagctgtggtttcagagtagtagcatcttgctgtggaactaacaacatttta-------caaattgataaaat----agGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG
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aatctttgaatatttcagcatcagcatattttctatgctagaagacaccttatgtatgttttattttgctttggtgtgattgtggtgataatgtttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTCTACATTGAGAGACTTG
upper sequence: AT5G56160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 4
gtacgagatatggtttcagctgtgg--tttcagagtagtagcatct------tgctgtggaa--ctaacaacattttacaaattgataaaat--------agGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG
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--attatttgcttttttaatctttgaatatttcagcatcagcatattttcaatgctagaagacaccggatacatgttttattttggttgggtgtttttgaagGATTTTGAATTTGGAGAGCTGGAAGAAGTATTGCAGTATTATCCTCAAGGGTACCATGGAGTTGATAAGGAAGGTAGGCCAGTTTACATTGAGAGACTTG
upper sequence: AT5G56160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S307_16V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------gtacgagatatggtttcagctgtggtttcaga-gtagtagcatcttgctgtggaactaaca-acattttacaaattgataaaatagGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG
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tacgtgcttcgacaccagtacatactgatttatgtgagggggcatatattgtctctttatatcacgattcttattcgcaagttgtgattcgttcgttcagGACTTCAAATTTACAGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGGGTGGATAAAGAAGGCAGGCCTGTGTACATTGAAAGAATTG
upper sequence: AT5G56160.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S169_81V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------gtac-gagatatggtttcagctgt--ggtttcagagtagtagcatct-tgctgtggaactaac-aacattttacaaattgataaaatagGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG
||| | | ||| || || | | || | | | || | | | || || | | | | | | | |||| ||| ||| | || | || |||||| | ||||||||||||||||||||||||| |||||||| || |||||| | ||||| || || |||
ttggttttaggatactggaacatgcttcgagatattggggtgctttacatgcccacatgtacaacggttctcattgatgatatttgtttcgtttcttcagGACTTCGTTTTTACTGAAATTGACAAAGTGAGGAATTACTATCCTCAAGGGTATCATGGAGTGGATAAAGAAGGCAGACCTGTGTATATTGAAAGGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagtagtagcatcttgctgtggaactaacaacattttacaaattgataaaatagGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG
taacaacattttacaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgagatatggtttcagctgtggtttcagagtagtagcatcttgctgtggaactaacaacattttacaaattgataaaatagGATTTCAATTTCAAAGAGTTGGATGAAGTGACAAGGCACTATCCTCAAGGGTATCATGGAGTTGATAAAGATGGGAGACCTATTTATATCGAGAGACTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG