Sequence
atgc intronic sequence ATGC exonic sequence...attgtgtgcattataggattatcaactcttaagtctctttttgcttattgtgtgattgagatacacaaataacagatgatgattgtgacgttttatgcagATCAAGTCGATTCCGACCAAGCCCGTTGAGGGGCAGAAGACCGGGACCAGTGGGTTGAGGAAGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os10g11140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G025854_T05 (Zea mays), 3'ss of exon 1
attgtgtgcattataggattatcaactcttaagtctctttttgcttattgtgtgattgagatacacaaataacagatgatgattgtgacgttttatgcagATCAAGTCGATTCCGACCAAGCCCGTTGAGGGGCAGAAGACCGGGACCAGTGGGTTGAGGAAGAAG
|| | | || | | || | ||| || | ||| | ||||||| | | | || |||| | || | ||| | |||| || |||||| || || ||||||||||| ||||||||||||||||| ||||| ||||| ||||||| |||
-tttttgaaacaatggtttaggggaccatcgagttgtcttgtacttttggtgtgatgcacaatctcacataa----tcattactgtaattttttgtgtagatcagTTCAATCCCGACCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG
upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 2
---attgtgtgcattataggattatca-actcttaagtctctttttgcttattgtgtgattgagatacacaaataacagatgatgattgtgacgttttatgcagATCAAGTCGATTCCGACCAAGCCCGTTGAGGGGCAGAAGACCGGGACCAGTGGGTTGAGGAAGAAG----------------------------------
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gtttctttttgaaacaatggtttaggggaccatcgagttgtcttgtacttttggtgtgatgcacaatctcacataa----tcattactgtaattttttgtgtagATCAGTTCAATCCCGACCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAGGTTCTCCATTTGATTGCTTCCGAGCTATGCAGAT
upper sequence: LOC_Os10g11140.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G025854_T03 (Zea mays), 3'ss of exon 1
---attgtgtgcattataggattatca-actcttaagtctctttttgcttattgtgtgattgagatacacaaataacagatgatgattgtgacgttttatgcagATCAAGTCGATTCCGACCAAGCCCGTTGAGGGGCAGAAGACCGGGACCAGTGGGTTGAGGAAGAAG
| | || | | || ||| || | ||| || | ||| | ||||||| | | | || |||| | || | ||| | |||| || |||||| || || ||||||||||| ||||||||||||||||| ||||| ||||| ||||||| |||
gtttctttttgaaacaatggtttaggggaccatcgagttgtcttgtacttttggtgtgatgcacaatctcacataa----tcattactgtaattttttgtgtagATCAGTTCAATCCCGACCAAGCCAGTTGAGGGGCAGAAGACTGGGACTAGTGGCCTGAGGAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgtgtgattgagatacacaaataacagatgatgattgtgacgttttatgcagATCAAGTCGATTCCGACCAAGCCCGTTGAGGGGCAGAAGACCGGGACCAGTGGGTTGAGGAAGAAG
aaataac putative branch site (score: 2)
acaaataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attgtgtgcattataggattatcaactcttaagtctctttttgcttattgtgtgattgagatacacaaataacagatgatgattgtgacgttttatgcagATCAAGTCGATTCCGACCAAGCCCGTTGAGGGGCAGAAGACCGGGACCAGTGGGTTGAGGAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG