Sequence
atgc intronic sequence ATGC exonic sequencegtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
Basic information
species | Oryza sativa |
transcript | LOC_Os07g46450.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G340359_T01 (Zea mays), 3'ss of exon 16
gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
| | || | |||||| | | |||||||| ||| | || |||| | | ||| ||||||||||||| | ||||||||| |||| |||||||| ||||||||||||||||||||||||||||||||| |||||||||| || ||
--gtgaggaaaagaatacatgcgcatc---agttcttgatttaggtgaatcttgcaacctaactatatatgtttctcagGCTAGAAGTAATGCAATCCTACAGGCAAGTTTAGAAAGAAGAAAACAAGCACTACATGAGCGCCGTGTGGCTCTGGAACAAAAT
upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G036872_T02 (Zea mays), 3'ss of exon 16
gtaca-aagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
||| || ||| ||| ||||| | | |||||||| ||| | || ||| | | || ||||||||||||||| ||||||||| |||| |||||||||||||||||||||||||||||||| ||||| ||| |||||||||| ||||||
gtaaggaaaagaagagtgcatgtgcatc---agttcttgatttatgtgaatcttgcaacttaactatatat-tttctcagGCTAGAGGCAATGCAATCCTACAGGCAAGTTTGGAAAGAAGAAAACAAGCACTACACGAGCGTCGTGTGGCTCTGGAACAGGAT
upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S271_62V6.1 (Physcomitrella patens), 3'ss of exon 16
-------------------------gtacaaagggaatagtacatgtatactcaagacttttgatttacagta-atactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
||||| | | | ||| | || | ||| | | | | | | ||| | ||||| | |||||||||||| |||||||| ||||||||||||||||| ||||| |||||||| || || |||| || || || |||
tccttcaccttcagaccaatctctactacaagttaaccttaatagttatggtgaaaatgttttactcatgtcatacgttcgtggtcttttg-----attgaacagGCAAAAGGAAATGCAATTTTACAAGCTAGTTTGGAAAGAAGAAAGCAAGCTCTACATGACCGTCGGCTGGCCCTTGAACAAGAT
upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S78_26V6.1 (Physcomitrella patens), 3'ss of exon 15
---------------gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaa--actaa---ttggaaatgcttct---cagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
| || | | || ||| | | ||| ||| || | | |||||| | | | | || |||| | | | ||||| | ||| |||||||| |||||||| || |||||||||||||| ||||| ||||||| || ||| |||| || || || |||
atcatcctgctccatattcagaagaaactttacccttcgatacaatgcttgtg--taaatgtaatattcacattattatattttggcattatgaataaacagGCGAAAGGGAATGCAATTTTACAAGCTAGCTTGGAAAGAAGAAAGCAAGCTTTACATGACCGTCGTCTGGCCCTTGAACAAGAT
upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ23838 (Selaginella moellendorffii), 3'ss of exon 15
gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
||||| | || || | | |||| | || || || || |||||| |||||||||||| | ||||| |||||||||||| |||| |||||||| || || ||||| | ||||| || |||||
----------------------gtactcgcgttcttccatgtt--attgtactga----tatgtgcaag-----cttagGCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCACGATCGCCGGCTCGCTCTTGAACAGGAC
upper sequence: LOC_Os07g46450.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ24423 (Selaginella moellendorffii), 3'ss of exon 15
gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
||||| | || | | | |||| | || || || || |||||| |||||||||||| | ||||| |||||||||||| |||| |||||||| ||||| ||||| | ||||| || || ||
----------------------gtactcgcg--ttcttgcatgttattgtactga----tatgtgcaag-----cttagGCTAAAGGAAATGCAATTCTTCAAGCGAGTTTGGAAAGACGAAAGCAAGCACTTCATGATCGCCGGCTCGCTCTTGAACAAGACMapped 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|58669247|gb|CK057933.1|CK057933EST: AAAGACTGGAGATCACAAAGAATGACCTCCAGATCAGAATCGCGAAAGAG GCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCA
genomic: AAAGACTGGAGATCACAAAGAATGACCTCCAGATCAGAATCGCGAAAGAGgtacaaaggg ... tgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
tgcttctc CT-rich tract
taatactaaaaactaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaagggaatagtacatgtatactcaagacttttgatttacagtaatactaaaaactaattggaaatgcttctcagGCTAGAGGAAATGCAATCTTACAAGCAAGTTTGGAAAGAAGAAAACAAGCACTACATGAGCGCCGTTTGGCTCTGGAGCAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG