Sequence
atgc intronic sequence ATGC exonic sequencegtctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g37080.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G170868_T01 (Zea mays), 3'ss of exon 3
------gtctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT
||| | ||| ||||||||| ||||||||| ||||| || | | || | | | | | | | ||| | | | | || || || |||| | | ||||| | ||| || ||| | ||| | | ||| |||| |||| | |||||| ||||||||||||||||| ||||||||||||||||||||||||||||||| ||||||||||||||||| ||| |||| || || |||||||||| ||||
gtatgtttcttatcttgaataacttttag---ctgttgtttcatgaatttgcaacatcattgtatcagtataggag--aacttcttagtcatcattgctga--tttgttaatt--tctttttctaactcctttca-taattcgta--gacaatgttttaactaaaatcttc--ttttccttcgtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGATGTTTTCCTGGAAGTAGGGAAGATGTCCAAGTACAGTCATTGTGATTGGCTT
upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G444643_T01 (Zea mays), 3'ss of exon 4
------gtctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT
|| | ||| ||||| ||| ||||||| ||| ||||| || | | || ||| | | |||| || ||| |||| | | || || | |||| | | || || | || |||| |||||| | |||||| || | ||| | |||||| ||||||||||||||||| |||||||||||||||||||||||||||| || ||||||||||||||||| ||| |||| || ||||||||||||| ||||
gtatgttccttatcttgaataactgttagattttgttattttgtgaatttgcaacatcatt--cttagtc--atcattgct-tatttgttaattcc------tttttctaactcatct---cataattcat---agacaatttttttaacaatc-----------ttctgatcttctccttggtcaaccagATTTGCTAGAGTTGGCTCTATAGTATTGGCAATTCATGATGCAAGTGACGTTTTCCTGGAAGTAGGGAAGATGTCCAAGTACAGCCATTGTGATTGGCTT
upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA08G36370.1 (Glycine max), 3'ss of exon 3
gtctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaata-ttttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT
| | || | | | | || | || || ||| || | | ||| | | | || | | | | || | | || | ||| || ||| | | ||||||||| | ||||| ||||| || || ||| |||||||||| || |||||||| ||||| ||||||||||| ||||||| || | ||| |
----------------------------------------------------------------------------gaaaattttggaactaattcccacactagttctatttttaat-------tttaatttaattctctggaaatttgatttggtt-tctcttctatgtttaacaa--attcagGTTTGCACGTGTTGGATCAGTGGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTGGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACTATG
upper sequence: LOC_Os02g37080.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G12080.1 (Glycine max), 3'ss of exon 3
gtctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT
|| || || | || | | | | ||| | | |||| || | | | ||| | | || | ||| ||||| | | | | | |||||||||| | ||||| ||||| || || ||| |||||||||| || |||||||| || || ||||||||||| ||||||| || | ||| |
------------------------------------------------------------------------------agaatt-gtggaactaattccca-cactagttctatttttattttaatttagttctctttg--gaaatttgat---tttgtttctcttctatgtttaacacattcagGTTTGCTCGTGTTGGATCAGTTGTTTTAGCACTTCATGATGCTAGCGATGTGTTTCTAGAGATAGGGAAAATGTCCAAATACAGTGGTGCTGAAACAATGMapped 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|88723508|gb|CI747018.1|CI747018EST: TCACATCATGTTGCAACTGTTGCGCTGATAGTTTTATCTTATGTGTTCAG GTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGT
genomic: TCACATCATGTTGCAACTGTTGCGCTGATAGTTTTATCTTATGTGTTCAGgtctcttttt ... catgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGT
EST:
gi|33683971|gb|CF312210.1|CF312210EST: TCACATCATGTTGCAACTGTTGCGCTGATAGTTTTATCTTATGTGTTCAG GTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGT
genomic: TCACATCATGTTGCAACTGTTGCGCTGATAGTTTTATCTTATGTGTTCAGgtctcttttt ... catgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT
tttttcttcat CT-rich tract
tttattaacacttaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctctttttgtctaacttttaatttttgttgtttcttgaatatgaactttttttaccttgattcaagcattactctatgagttagtagcacagggccttaatattttatcttcactgagtttatttcactcatttttattaacacttaactaatttatttctgaaatttttcttcatgaaccagGTTTGCTAGAGTTGGCTCAGTAGTATTGGCAATTCATGATGCAAGTGATGTGTTCCTGGAAGTAGGGAAAATGGCCAAATATAGCCATTGTGATTTGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG