Sequence
atgc intronic sequence ATGC exonic sequencegtatcttctgtcattcttctccatttttattcttttatcagattattaagccctagtttctaaaaaaatgttgatgtgtttaatcagGAACCTAATGTGAGCATGATCATCACGGACTACTGGATGCCGGAGATGACCGGGTACGACCTGCTCAAGAAGATCAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os07g26720.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g26720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G148056_T01 (Zea mays), 3'ss of exon 2
gtatcttctgtcattcttctccatttttattcttttatcaga--------ttattaagccctagtttctaaaaaaatg-----------ttgatgtgtttaatcagGAACCTAATGTGAGCATGATCATCACGGACTACTGGATGCCGGAGATGACCGGGTACGACCTGCTCAAGAAGATCAAG
||| || ||| ||||||| || | | | || || ||||| | |||| | || || || ||| || ||||| || |||||||||||||||||||| |||||||||||||| ||||||||||| |||||||||||||| ||| |||||
gtacctgctgc---tcttctcagttctcactgacgaataggaaaaagacattattggattttcgtttggatgaacctgaactttgccttttctcttgtgtatccagGAGCCGAATGTGAGCATGATCATCACAGACTACTGGATGCCAGAGATGACCGGCTACGACCTGCTCAAAAAGGTCAAG
upper sequence: LOC_Os07g26720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ14702 (Selaginella moellendorffii), 3'ss of exon 2
-----------------------------------------------------------------------------------------------------------gtatcttctgtcattcttctccatttttattcttttatcagattattaagccctagtttctaaaaaaatgttgatgtgtttaat-cagGAACCTAATGTGAGCATGATCATCACGGACTACTGGATGCCGGAGATGACCGGGTACGACCTGCTCAAGAAGATCAAG
|| | || | | | | | || || | | | | || | ||| | | || ||| | |||| ||| | | | |||||||||||||||| || |||||||| ||||| || || || |||||||||||| |||||
gttcgtgctcttcttctttcttgtgctggattgaaaactcgttaaatcgttgtcgcttgatctgtatggaatgaaaaaaaaggtgatagctttgttgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG
upper sequence: LOC_Os07g26720.2 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ14701 (Selaginella moellendorffii), 3'ss of exon 2
------------gtatcttctgtcattcttctccatttttattcttttatcagattattaagccctagtttctaaaaaaatgttgatgtgtttaat-cagGAACCTAATGTGAGCATGATCATCACGGACTACTGGATGCCGGAGATGACCGGGTACGACCTGCTCAAGAAGATCAAG
|| | || | | | | | || || | | | | || | ||| | | || ||| | |||| ||| | | | |||||||||||||||| || |||||||| ||||| || || || |||||||||||| |||||
tgggtggttgtggtggtgttggtggatgctagctaagctaatctttggctgatttcctcgagattttctttgcttcctctggcttttgcttttgttgcagGCCATTAAAATAAACTTGATCATCACGGACTATTGTATGCCGGAAATGACAGGCTATGATCTGCTCAAGAAGGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttatcagattattaagccctagtttctaaaaaaatgttgatgtgtttaatcagGAACCTAATGTGAGCATGATCATCACGGACTACTGGATGCCGGAGATGACCGGGTACGACCTGCTCAAGAAGATCAAG
tagtttctaaaaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcttctgtcattcttctccatttttattcttttatcagattattaagccctagtttctaaaaaaatgttgatgtgtttaatcagGAACCTAATGTGAGCATGATCATCACGGACTACTGGATGCCGGAGATGACCGGGTACGACCTGCTCAAGAAGATCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA