Sequence
atgc intronic sequence ATGC exonic sequencegtgataaactaaattatctactaatcatcattcatcagtcaacactcaccactcctcttctctttctctgttttatattagtgctttgcatgtacacgttgccatgtccgtgatgctgcatatatgttgtgtttgtgttttgtagGGCCTGGCGATCCTGAGGGCCTCGCTGCAGTCCAAGACCGTTCTCAGCGACGTTTTCCTTGCCAGGAGGCCTGCAAAGCAAGCCTGA
Basic information
species | Oryza sativa |
transcript | LOC_Os01g06030.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g06030.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G102822_T01 (Zea mays), 3'ss of exon 1
gtgataaactaaattatctactaatcatcattcatcagtcaacactcaccactcctcttctctttctctgttttatattagtgctttgcatgtacacgttgccatgtccgtgatgctgcatatatgttgtgtttgtgttttgtagGGCCTGGCGAT--CCTGAGGGCCTCGCTGCAGTCCAAGACCGTTCTCAGCGACGTTTTCCTTGCCAGGAGGCCTGCAAAGCAAGCCTGA
| ||| | | | || || | | | | || | | | | ||| | | || | | | | | | || | ||| | ||||| || || | || || | || | | ||| | |||||||||||||||||||| |||||||| ||||| || ||||| | ||||| | | || |||
------------gtcatcgagttaaactcttttgtt---------ttggttttagttttatatatatgtgtgtaaaataaatatatgaaactttgtagctgtaaaaaagctgacgg-gcataaat-ttttaattttgctgccagGGTTTTAGAGATTTCTCCAGGGCCTCGCTGCAGTCCAAAACCGTTCTGAGCGATGTGTTCCTCGGCAGGAAAGATCGCGGTGATGCTTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtacacgttgccatgtccgtgatgctgcatatatgttgtgtttgtgttttgtagGGCCTGGCGATCCTGAGGGCCTCGCTGCAGTCCAAGACCGTTCTCAGCGACGTTTTCCTTGCCAGGAGGCCTGCAAAGCAAGCCTGA
atatatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgataaactaaattatctactaatcatcattcatcagtcaacactcaccactcctcttctctttctctgttttatattagtgctttgcatgtacacgttgccatgtccgtgatgctgcatatatgttgtgtttgtgttttgtagGGCCTGGCGATCCTGAGGGCCTCGCTGCAGTCCAAGACCGTTCTCAGCGACGTTTTCCTTGCCAGGAGGCCTGCAAAGCAAGCCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG