Sequence
atgc intronic sequence ATGC exonic sequence...gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggcatggatgactcttctcattgaaacttttggtgatctcttggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os08g38320.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA15G12760.1 (Glycine max), 3'ss of exon 2
-gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggcatgg-atgactcttctcattgaaacttttggtgatctcttggta--tttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT
||| || | | | | || | |||| | ||| | ||| |||| | | || | | | || | || || | ||| || ||| || |||||||||||||| || || || || || || || || |||||||||||| | |||||||| || || ||||||||||| ||||| |||| |||
tgatttcttttcttgctttgcatttttgggttttttgcctggtttggcaattatgttatgatt----tgatggtatccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTTCTTGTTAGGGATGAT
upper sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA09G01800.1 (Glycine max), 3'ss of exon 2
---gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggcatgg-atgactcttctcattgaaacttttggtgatctcttggta--tttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT
|| || ||| || || | || | |||| || ||| | ||| |||| | || ||| || | || || | ||| || ||| || |||||||||||||| || || || || || || || || |||||||||||| | |||||||| || || ||||||||||||||||| ||||| ||
ttatttcttttcttgcttttgaatt--ttgggtattttgcccggtttggcaattatgttatgattgg----atgctaaccactgctaatttccttgtaacttgcagATTTTATGTGGCAGAGGTCCTACTGGCTTTGGAGTATCTTCACATGCTTGGGATTGTCTACCGTGACCTTAAGCCAGAAAATGTCCTTGTTCGGGATGAC
upper sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G55910.1 (Arabidopsis thaliana), 3'ss of exon 2
gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggcatggatgactcttctcattgaaacttttggtgatctcttggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT
|| | | | | | |||| | | | || | | | | | || || || | |||| | || | || |||||| ||||| || || || ||||||||| | ||||| | || ||||||||||| || ||||||||||||||||| || || || ||||| | || |||
-----------gtaagaaactttttctaaactttctt---tatctaagaatctagttttgtgcgtttatataacct--tagtgacttgctgtt-ttgcagGTTTTATGTCGCGGAAGTGCTTCTTGCAATGGAATATTTACACATGCTTGGGATCATTTACCGTGATCTGAAACCCGAGAACGTTCTTGTGAGAGATGAT
upper sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT4G26610.1 (Arabidopsis thaliana), 3'ss of exon 2
gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggca-tggatgactcttctcattgaaac--ttttggtgatctcttggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT
| || | || ||| || | | ||| || || | || | | | || | || ||| | |||| | | | | || |||||| ||||| || || || ||||||||| | ||||| || ||||||||||| || |||||||| ||||| || ||||| ||||| ||||| | || |||
-gtaaaaacattttgaataatcagtt--tcatgttttgcatccaagataccactttttttttttttttgttaaaatcatattggctttgtttacattttccagGTTTTATGTAGCGGAAGTACTTCTTGCAATGGAATATCTTCATATGCTTGGCATCATATACCGCGATCTAAAGCCAGAGAATGTTCTTGTTAGAGATGAT
upper sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv19s0015g00770.t01 (Vitis vinifera), 3'ss of exon 1
--gatcaattgttgtttgctaactcattaatt---ctttttggcgtcttgaaaggcatggatgactcttctcattgaaacttttggtgatctcttggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT
| ||| || || || || || || || | | | || || |||| | | | | || | | |||| || | | |||||||||||| ||||||||||||||||| | |||||||| || |||||||||||| | || ||||| ||||| ||||| ||||||||||| |||| ||
agaagcaaatgaagtcatctttcttgtttgttgagctaatcagttttttaaagttcatgtgggcttgtgattatcgttaactttg-----ctttgcaacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGACMapped 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|58679820|gb|CK068507.1|CK068507EST: ACTCTTCGACAAAGGCAGCCTGGAAAGCATTTCTCAGAGCAAGCAGCAAA GTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGG
genomic: ACTCTTCGACAAAGGCAGCCTGGAAAGCATTTCTCAGAGCAAGCAGCAAAgtatgtgaca ... ggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGG
EST:
gi|29635735|gb|CB640744.1|CB640744EST: ACTCTTCGACAAAGGCAGCCTGNAAAGCATTTCTCAGAGCAAGCAGCAAA GTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGG
genomic: ACTCTTCGACAAAGGCAGCCTGGAAAGCATTTCTCAGAGCAAGCAGCAAAgtatgtgaca ... ggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaggcatggatgactcttctcattgaaacttttggtgatctcttggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT
tctcttg CT-rich tract
aaactttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatcaattgttgtttgctaactcattaattctttttggcgtcttgaaaggcatggatgactcttctcattgaaacttttggtgatctcttggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT