Sequence
atgc intronic sequence ATGC exonic sequencegtaatgccactctagctcacatcaattcattcagattgattgtccttgcttatatcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
Basic information
species | Oryza sativa |
transcript | LOC_Os10g29660.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G092916_T01 (Zea mays), 3'ss of exon 4
gtaatgccactctagctcacatcaattc-attcagattgattgtccttgcttatatcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
||||||| | | ||| ||| || |||| || | | | || | || || | | || ||||||||||||||| |||| || || ||||| |||||||| |||| ||||||||||| ||||||||||| |||| | ||| | | | |
gtaatgcttttgtcactctgatcgatcggattcctgctgctgctggtctctcacattgactcaatgggttcttctgacatgcagGATTTCAAGGTCCAAAATATAGTTGGGTCATGTGACCTCAAGTTTCCTATTCGTCTGGAGGGCCTCGCTTTGGCCAGTGGTTTGTCTGCCACT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G466938_T01 (Zea mays), 3'ss of exon 4
gtaatgccactctagctcacatcaattcattcagattgattgtccttgcttatatcagcttgacgcattgg---aacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
||||||| | | ||| ||| || | |||| | | | || | || || | | || |||| ||||||||||||||| |||| || || ||||| |||||||| |||| ||||||||||| ||||||||||| |||| | |||| | | | |
gtaatgcttttgtcactctgatcgat-----cggattcctgctggtctctcacattgactcaatgggttcttctgacat-atgcagGATTTCAAGGTCCAAAATATAGTTGGGTCATGTGACCTCAAGTTTCCTATTCGTCTGGAGGGCCTCGCTTTGGCCAGTGGCTTGTCTGCCACT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G25450.3 (Glycine max), 3'ss of exon 6
------------------gtaatgccactctagctcacatcaattcattcagattg-attgtccttgcttatatcagcttgacgcattgg--aacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
| | ||| | | | ||| | | | |||| |||| ||| | ||| | |||| | ||| | |||||||||| || ||||||||||| || || ||||||||||| || || || || |||||||| ||||| ||||| ||||| || ||||| |||
gtactgcttttgctctttctcaatccatgttttttgttcttttctcactgtaactatgttgtgcttgatta---ctaattggttccttgggtattatgctctagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
--------gtaatgccactctagctcacatcaattcattcagatt-------gattgtccttgcttat--atcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
|| | | | | |||| || || | | || || | || || | | | || | ||||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| || ||||| |||
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G28780.1 (Glycine max), 3'ss of exon 6
--gtaatgcc-actct--agctcacatcaattcattcagatt-------gattgtccttgcttat--atcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
|| | ||||| | | |||| || || | | | || || | || || | | | || | ||||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||| ||| | || ||||| |||
gtacaacatctactctgaaaattttatcagttgttttccactctacagaagtagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATAGTGCTTTCTCAAGT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G04500.1 (Glycine max), 3'ss of exon 6
--------------------------------------------------------------------------------gtaatgccactctagctcacatcaattcattcagattg-attgtccttgcttatatcagcttgacgcattgg--aacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
|||| ||| | | | | ||| | ||| | || ||| ||| | ||| | |||| | ||| | |||||||||| || ||||||||||| || || ||||||||||| || || || || |||||||| ||||| ||||| ||||| || ||||| |||
gtactgcttctgctctttctcataatctttgctgaaattattgaaaagcgctattttaaaaattttctattttcccccatttaat-ccattttggtcgttcttttctcactataattatgtagtgtttgatta---ctaattggttctttgggtattatgctttagGATTTCAAAATTCAGAACATTGTCGGCTCTTGTGATGTCAAGTTCCCCATACGGCTGGAGGGTCTTGCATATTCCCATGGTGCTTTCTCAAGT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA09G41330.1 (Glycine max), 3'ss of exon 6
--gtaatgccactctagctcacatcaattcattcagatt-------gattgtccttgcttat--atcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
|| | | | | |||| || || | | || || | || || | | | || | ||||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| || ||||| |||
gttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
--gtaatgccactctagctcacatcaattcat--tcagattgattgtccttgcttatatcagcttgacgca-ttggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
||| | | | || | || || | || || ||||||||| | | | || ||| |||| |||||||||||||||| ||||| ||||| ||||| |||||||||||||| ||||| | || || || |||||||| ||||| | || ||||| |||
gtacaatttctttaaaccttttccctatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------------------gtaatgccactctagctca--catcaattcattcagattgattgtcc----------ttgcttatatcagct--tgacgcattgga-----acatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
|| || | | || |||| || |||||| | ||| || || || | |||| || | | | | | |||| |||||||||| ||||| ||||||||||| || ||||||||||||||||| || ||| | || || || ||||| || |||||| | || ||||| |||
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtattt-ttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------gtaatgccactctagctcacatcaattcattca--gattgattgtccttg--cttatatcagcttgac----gcattggaacatg--atgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
| |||| | | | | | | || | || ||| | || ||||| | | ||||| | || | || ||| ||||||| ||||| |||||||| ||||| || |||||||| ||||| || || | || || |||||||| ||||||||||| || || || ||
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctattcttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------gtaatgccactctagctcacatcaattcattcagattgattgtccttgcttatatcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
| | | | || | | | ||| | | ||| | | | | | || | | | | | |||||||||| || || ||||| ||||||||||||||||| |||||||| ||||| || || || || | ||||| |||| || || || |||
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcctagct-attgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5
gtaatgccactctagctcacatcaattcattcagattgattgtccttgcttatatcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
| | | || |||| | ||| ||| | | | ||| || | ||||||||| |||||||||||||||||||| || ||||| || || || || || | |||||||||| || || |||| || ||||| ||
----------------gtatgaagacgaaaacacattg-tggtctgagctcaaacttagt-aacgtccgtgatc-----gcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
upper sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
gtaatgccactctagctcacatcaattcattcagattgattgtccttgcttatatcagcttgacgcattggaacatgat-gcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
| | | || |||| | ||| ||| | | | ||| |||||| ||||||||| |||||||||||||||||||| || || || || || || || || | |||||||||| || || |||| || ||||| ||
----------------gtatgaagaagaaaacacattg-tggtctgagctcaaacttagt-aacgtc------catgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|8324452|gb|AU091604.1|AU091604EST: CNCAGTATGCGCGAATCGTCCAAAAGCTTGGCTTCCCAGCAAAGTTCAAG GATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATT
genomic: CGCAGTATGCGCGAATCGTCCAAAAGCTTGGCTTCCCAGCAAAGTTCAAGgtaatgccac ... catgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attcagattgattgtccttgcttatatcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
gcttgac putative branch site (score: 4)
ttatatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgccactctagctcacatcaattcattcagattgattgtccttgcttatatcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG