Sequence
atgc intronic sequence ATGC exonic sequencegttagttttgtgaaattttataccactgtcataatttaggcatggagacaatcagttgtatcttaagaatcctttattgataatatattgtttgggttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05030.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os07g47100.2 (Oryza sativa), 3'ss of exon 8
gttagttttgtgaaattttataccactgtcataatttaggcatggagacaatcagttgtatcttaagaatcctttattgataatatattgtttggg--ttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
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----gtgtgcctctgctttgatgcagtatcaaaatttgcatatagtttcatt---ttatagtttga-----ttttatctactttgt-ttgtttgatattggcagTTGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAA
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 9
gttagttttgtgaaattttataccactgtcataatttaggcatggagacaatcagttgtatcttaagaatcctttattgataatatattgtttgggttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
|| | | || ||||| | || | | |||| || | || | | | ||| | |||| | | || ||||| | | ||||||| || || ||||| || |||| ||| || || ||||| |||||||||||||| ||||| || || ||||| || ||||||||||
-ttggcagtctgtaatttctttaatctcactttgcaccagcatcttccaaagtacatgatattgatattttttttgaccctttcatat-atatatatttcagCTGCTAGATCTGAGTGGCATTCTCACTGTGTTCTTCTCTGGAATAGTAATGTCACATTACACTTGGCATAATGTGACAGAAAGCTCTAGGATTACTACCA
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G027851_T03 (Zea mays), 3'ss of exon 6
gttagttttgtgaaattttataccactgtcataatttaggcatggagacaatcagttgtatcttaagaatc--ctttattgataatatattgtttgggttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
||| | | | | ||| || || || | | || || | || || | || ||| ||||| | | |||||||| | | ||||||| || || || ||||| ||||| || || |||||||| |||||||| ||||||||||| || |||||||||||| | || ||||
---------gtgcacctctgatcagatgtggcaa---gggaattcacgcttgttgtcttactctcttaactgactctgttcata-tatatggcat---ttgcagCTGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCA
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------gttagttttgtgaaatttt---ataccactgtcataatttaggcatg-gagacaatcagttgtatcttaagaatcct---ttattgataatatattgtttgggt-----------tgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
| ||| ||| |||| ||| | | | | | |||| || ||| | ||| |||| || | ||| | || | || ||||||| ||| ||||||||| || || | || || || ||||| ||||| ||||| |||||||||||||| |||||||| || | || ||| || ||||
gtcagtttgaccttctatgtggattgttcgtccaattatctgttcctggaatttttcaaatagatcgatgaggaaatgagcatacgatttggattgttacaacttgtaaatctgaaattttcagaaattttactttcgcgtgtcgtcattggtgcagCTTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCA
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ05720 (Selaginella moellendorffii), 3'ss of exon 7
gttagttttgtgaaattttataccactgtcataatttaggcatggagacaatcagttgtatcttaagaatcctttattgataatatattgtttgggttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
|| ||| ||| || | | | || | || || || ||| | || | || ||||| ||| | ||||||| ||||| || || || || ||||| ||||| ||||| ||||| || |||||||| ||||| |||||||||||||| || ||||
---------------------------gtgatagtttttttctgtatagag--aggt--------agcatttcttcttgttctcatgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA
upper sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ32893 (Selaginella moellendorffii), 3'ss of exon 7
gttagttttgtgaaattttataccactgtcataatttaggcatggagacaatcagttgtatcttaaga----atcctttattgataatatattgtttgggttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
|| | ||||| || || || ||| | || | || ||||| ||| | ||||||| ||||| || || || || ||||| ||||| ||||| ||||| || |||||||| ||||| |||||||||||||| || ||||
-----------------------------------------gtgagagtttttttctgtatagagaggtagcatttcttcttgttctcatgcgtatgccattccagCTGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaatcagttgtatcttaagaatcctttattgataatatattgtttgggttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
tattgat putative branch site (score: 3)
ttaagaatcctttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttttgtgaaattttataccactgtcataatttaggcatggagacaatcagttgtatcttaagaatcctttattgataatatattgtttgggttgcagCTATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA