Sequence
atgc intronic sequence ATGC exonic sequencegtaatccccgatatcccgattcgcgccctcgctcgattgtcgtttccgcacccccttctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g17180.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 1
gtaatccccgatatcccgattcgcgc-cctcg------ctcgattgtcgtttccgcaccccctt--------ctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
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gtaatcgcgccccctccaattcgtgcgcttcgattttcctatatttctgtttacttgttctattgcagatatttttcctgattgtggatgttatggtgattagATGCGGACATGGAGGACTACGGGTTCGAGTACTCTGACGAAGAGCCGGAGGAGCAGGATGTCGACATTGAGAACCAGTATTACAACTCCAAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 1
gtaatccccgatatc-ccgattcgcg-------ccctcgctcgattgtcgtttccgcaccccc--------ttctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
|||||| |||| | |||| ||| | ||| | |||| | || | | | || | || | | || | | | ||||||||| |||||||| ||||||||||||||||| ||||| |||||||||||||||||||| || |||||||||||||| |||||||| ||||
gtaatc--cgatccctccgactcgtgggctaaattctctattatttgtggcttgttctcttgcggagaattttttttcttgatcatggatgttatggtgattagATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 1
gtaatccccgatatcccgattcgcgccctcgctcgattgtcgtttccgcacccccttctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
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----------gta-cgcgcttgttgttgttgttgattaatgcatttggtgttatgatgatgaaactaattgattgattgactgtgtagATGCTGACATGGAGGACTACGGTTTCGAGTACTCCGATGAGGAGGAAGTGGAGCAAGACGTTGATATCGAGAATCAATATTACAATTCAAAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G26990.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------gtaatccccgatatcccgattcgcgccctcgctcgattgtcgt-ttccgcacc-----cccttctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
|||| | | ||| || ||| || | || || | | || | || || ||| || || | |||||| ||||||||||| || || |||||||| || || || |||| ||||| || ||||||||||| ||||||||||| || ||||| ||||
gtcttgttcttgttttgctatgtctaatcttctactctgaaacaatctagggttcgaaagttcccgaattcgactacttactttgttacgaatcgatagtgttttattgatttgggttttcgattt-ttgtgtagATGCTGACATGGAGGACTATGGATTCGAGTATTCTGATGAGGAGCAAGAGGAACAAGATGTTGACATTGAGAACCAGTATTATAACTCTAAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 1
gtaatccccgatatcccgattcgcgccctcgctcgattgtcgtttccgcacccccttctctcatccccgtgatcggtt------------ccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
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gtatccttgaaagtgcaaattctttctctcatacagatgcttaatttattctgtaatggtttgttaataaaatgatttggaattctttggcattctgtagATGCAGACATGGAGGATTATGGATTTGAGTACTCAGAAGAGGAGCCTGAGGAGCAGGATGTTGATATTGAGAATCAATATTACAATTCTAAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 1
--------gtaatccccg-atatcccgattcgcgccctcgctcgattgtcgt---ttccgcacccccttctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
|| | ||| || | || ||||| | | | | || | | | || | || |||||||||| ||||| ||||| || || ||||| || || || ||||| || ||||| ||||||||||||||||| ||||||||||| | ||||
gctagtacgtgacaaggatatacttgaatctgtgcgtgacggttattgtactaggtattgtaagtagctcatggttttcttttgatggatgtcattgcagATGCGGATATGGAAGATTATGGCTTTGAGTATTCTGATGAGGAGCCTGAAGAGCAAGATGTTGACATCGAGAATCAGTACTACAATACTAAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------gtaatccccgatatcccgattcgcgccctcgctcgattgtcgtttccgcacccccttctctc-atccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
| | | || | ||| | | | | | || || || || || | | || | | ||||||| |||||||| ||||| ||||||||||| || ||||| || || |||||||| |||||||| || ||||| || || || || ||||||
tcccgaaggcaaagacatactccacccagcttcattataatggtgaactatatatttgtttccttatttaatcgatgtcttttgctggacctgatcacagATGCCGACATGGAAGATTATGGGTTCGAGTATTCGGACGAGGAACCCGAGGAGCAAGATGTTGATATTGAGAATCAATATTATAATACCAAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ29478 (Selaginella moellendorffii), 3'ss of exon 1
gtaatccccg---atatcccgattcgcgccctcgctcgattg-tcgtttccgcacc---cccttctctcatccccg--------tgatcggttccttt---tccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
|||| | | || | | | | | || ||||| | | | |||| | | | | |||| | || | |||| | | | ||| ||||||||||| ||||| || || |||||||| || || || || |||||||| ||||| || |||||||| |||||||||||||| ||||
gtaagctctcttcgtagcgcagcgctcactagggcgcgatttcttgctcccgcgcttggcattgcatggatcctcagtaattcttgcttggtttcgtggtgtatagACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAG
upper sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ28052 (Selaginella moellendorffii), 3'ss of exon 1
gtaatccccg---atatcccgattcgcgccctcgctcgattg-tcgtttccgcacc---cccttctctcatccccg--------tgatcggttccttt---tccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
|||| | | || | | | ||| || ||||| | | | |||| | | | | |||| | || | |||| | | | ||| ||||||||||| ||||| || || |||||||| || || || || |||||||| ||||| || |||||||| |||||||||||||| ||||
gtaagctctcttcgtagcgcagcgctcgctagggcgcgatttcttgctcccgcgcttggcattgcatggatcctcagtaattcttgcttggtttcgtggtgtatagACGCGGACATGGAAGATTATGGCTTTGAGTACTCGGAAGAAGACCCCGAGGAGCAAGATGTCGATATCGAGAATCAGTACTACAACTCTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgattgtcgtttccgcacccccttctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
tcggttccttttcc CT-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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatccccgatatcccgattcgcgccctcgctcgattgtcgtttccgcacccccttctctcatccccgtgatcggttccttttccagATGCGGACATGGAGGATTACGGGTTCGAGTACTCCGACGACGAGCCGGAGGAGCAGGATGTTGACATCGAGAACCAGTACTACAACTCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG