Sequence
atgc intronic sequence ATGC exonic sequencegtatgtatgagccatggtggtggcgggggagctgatctcgaacctccagatttgggggctagggtttgtgctctaatggggatgcactttgttgtgcgtgtgtgtagGGAGCAGGATGGGTACGAGGTGCTGCGCAAGCTTGGGAGGGGGAAGTACAGCGAGGTGTTCGAGGGATTCCGGCCCGGGGGTGACGAGAGGTGCGTTATT
Basic information
species | Oryza sativa |
transcript | LOC_Os03g55490.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g55490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G154799_T01 (Zea mays), 3'ss of exon 1
gtatgtatgagccatggtggtggcgggggagctgatctcgaacctccagatttgggggctagggtttgtgctctaatggggatgcactttgttgtgcgtgt--gtgtagGGAGCAGGATGGGTACGAGGTGCTGCGCAAGCTTGGGAGGGGGAAGTACAGCGAGGTGTTCGAGGGATTCCGGCCCGGGGGTGACGAGAGGTGCGTTATT
|| | || || || |||| || | | | | | | |||| | || | | || || | ||| ||| ||| ||||||||||||||||||||||||| ||| | ||||||||||||||||||||||||||||| || |||||| ||||| | || ||||| ||||| |||
----------------gtaggcgcacggagctggagctcgg--ctttacactgtgatccccagatttgaatggtgtaaggttttatttctgatgcgtctgtccgtgcagGAAGCAGGATGGGTACGAGGTGCTGCGGAAGGTGGGGAGGGGGAAGTACAGCGAGGTGTTCGAAGGGTTCCGGGCCGGGAGCGATGAGAGATGCGTCATT
upper sequence: LOC_Os03g55490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G112056_T01 (Zea mays), 3'ss of exon 1
gtatgtatgagccatggtggtggcgggggagctgatctcgaacctccagatttgggggctagggtttgtgctctaatggggatgcactttg--ttgtgcgtgtgtgtagGGAGCAGGATGGGTACGAGGTGCTGCGCAAGCTTGGGAGGGGGAAGTACAGCGAGGTGTTCGAGGGATTCCGGCCCGGGGGTGACGAGAGGTGCGTTATT
|| | | || || |||| || | | || | | | |||| | || | | || | || || ||| ||| ||||||||||||| ||||||||||| ||| | ||||||||||||||||||||||||||||| || ||| || || || | || ||||| ||||| |||
----------------gtaggcacatggagctggagctcgg--ctttacactttgatccccagatttgaatggtgtaaggttttatttctgattcgtctgtccgtgcagGAAGCAGGATGGGTATGAGGTGCTGCGGAAGGTGGGGAGGGGGAAGTACAGCGAGGTGTTCGAAGGGTTCTGGGCCAGGAGCGATGAGAGATGCGTCATT
upper sequence: LOC_Os03g55490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G138774_T01 (Zea mays), 3'ss of exon 2
gtatgtatgagccatggtggtggcgggggagctgatctcgaacctccagatttgggggctagggtttgtgctctaatggggatgcactttgttgtgcgtgt--gtgtagGGAGCAGGATGGGTACGAGGTGCTGCGCAAGCTTGGGAGGGGGAAGTACAGCGAGGTGTTCGAGGGATTCCGGCCCGGGGGTGACGAGAGGTGCGTTATT
|| | | | || |||| || | | | | | | |||| | || | | || || | ||| || ||| ||||||||||||||||||||||||| ||| | ||||||||||||||||||||||||||||| || |||||| |||| | || || || ||||| |||
----------------gtaggcacacgaagctggagctcgg--ctttacactgtgatccccagatttgaatggtgtaaggttttatttctgatgcgtctgtccatgcagGAAGCAGGATGGGTACGAGGTGCTGCGGAAGGTGGGGAGGGGGAAGTACAGCGAGGTGTTCGAAGGGTTCCGGGTCGGGAGCGATGAAAGATGCGTCATT
upper sequence: LOC_Os03g55490.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EDO97438 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtatgtatgagccatggtggtggcgggggagctgatctcgaacctccagatttgggggctagggtttgtgctctaatggggatgcactttgttgtgcgtgtgtgtagGGAGCAGGATGGGTACGAGGTGCTGCGCAAGCTTGGGAGGGGGAAGTACAGCGAGGTGTTCGAGGGATTC--CGGCCCGGGGGTGACGA----GAGGTGCGTTATT-------------
| | || | | | || | | | || | ||| || | | || || | | | ||||| |||| ||| ||||| | |||||||| ||||||||||||||||| || || | | || | || || ||| | ||
------------------------gcctcacacgacattcagcacgcactcgcccttac-attgcttat-ctcacccaggagtatagttccttaccttcacaccgtcatcctcgcacccttggcagGTGGTGCGGAAGGTTGGGCGAGGGAAGTATAGCGAGGTGTTCGAGGGCGTCAACGTTGCAGCGGAGCCGCCCACGAAATGCATCATCAAAATCCTGAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgggggctagggtttgtgctctaatggggatgcactttgttgtgcgtgtgtgtagGGAGCAGGATGGGTACGAGGTGCTGCGCAAGCTTGGGAGGGGGAAGTACAGCGAGGTGTTCGAGGGATTCCGGCCCGGGGGTGACGAGAGGTGCGTTATT
ctctaat putative branch site (score: 3)
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtatgagccatggtggtggcgggggagctgatctcgaacctccagatttgggggctagggtttgtgctctaatggggatgcactttgttgtgcgtgtgtgtagGGAGCAGGATGGGTACGAGGTGCTGCGCAAGCTTGGGAGGGGGAAGTACAGCGAGGTGTTCGAGGGATTCCGGCCCGGGGGTGACGAGAGGTGCGTTATT
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