Sequence
atgc intronic sequence ATGC exonic sequencegtgaaaaaatatctttaatgttgaacgcatcacttcaaactgttccattttcctaaaataaatacctgacttaatttgtgcgtaacaaacaaaaagcttccacttcttgaactgaggcactacctgcgagaagaaatgaattgttgaattttgttctaaatggtgcagGTGCATGTTCAGTCAGATCCTGCTGGGCGTCTGGTTATAACTGGGGACCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCATTCAAGAAG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g48370.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G110109_T01 (Zea mays), 3'ss of exon 10
gtgaaaaaatat-----ctttaatgttgaacgcatcacttcaaactgttccattttcctaaaataaatacctgacttaatttgtgcgtaacaaacaaaaagcttccacttcttgaactgaggcactacctgcgagaagaaatgaattgttgaattttgttctaaatggtgcagGTGCATGTTCAGTCAGATCCTGCTGGGCGTCTGGTTATAACTGGGGACCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCATTCAAGAAG
|||| || ||| | || |||| || || || || || |||| ||||| |||||| | | || || | | ||||| | | | | |||| | |||| | || ||| ||| | | || ||||||||| | | ||||||||||||||| |||||||||||||| ||||||||||| || ||||| ||||||||||||||||||||||||||||||||||| |||||||||
gtgaggaagtatggtgccattcatgtggagagccgagttttgaaacttttcattgacctaagataaatccttccagagataaatggagcataggcaaaaggaattttccttatgaaataaggccatgcca--tagaggaatttgctaatt---ttttgttctgacggtagcagGTGCATGTTCAATCAGATCCTGCTGGACGTCTGGTTATCACAGGGGATCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCGTTCAAGAAG
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G161854_T01 (Zea mays), 3'ss of exon 1
gtgaaaaaatatctttaatgttgaacgcatcacttcaaactgttccattttcctaaaataaatacctgacttaatttgtgcgtaacaaacaaaaagcttccacttcttgaactgaggcactacctgcgagaagaaatgaattgttgaattttgttctaaatggtg-cagGTGCATGTTCAGTCAGATCCTGCTGGGCGTCTGGTTATAACTGGGGACCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCATTCAAGAAG
| ||| | | | | || | | | | | || |||||| | || ||| ||| ||| | | |||| | |||||| |||||||||||||| |||||||||||||| | ||||||||| | ||||| ||||||||||||||||||||| |||||||||||| |||||||||
-------------------------------------------------------------gttggtgaacattctcgcactcccagagcagattgaatttttcttatcaaatgaggccatgccatagaggaga------ttgctaatttttcgttctcatggtggcagGTGCATGTTCAATCAGATCCTGCTGGACTTCTGGTTATCATAGGGGATCCAGAGCAGCCTGATAATCCTAAGGGGATCACTCCGTTCAAGAAG
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G180223_T01 (Zea mays), 3'ss of exon 3
gtgaaaaaatatctttaatgttgaacgcatcacttcaaactgttccattttcctaaaataaatacctgacttaatttgtgcgtaacaaacaaaaagcttccacttcttgaactgaggcactacctgcgagaagaaatgaattgttgaattttgttctaaatggtgcagGTGCATGTTCAGTCAGATCCTGCTGGGCGTCTGGTTATAACTGGGGACCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCATTCAAGAAG
| ||| | | | | || | | | | | || ||||| | | | ||| || || | || ||||||||| | | ||||||||||||||| |||||||||||||| ||| ||||||| || ||||| ||||||||||||||| |||||||||||||||||| |||||||||
-------------------------------------------------------------gttggtgaacattctcgcactcccagagcagattgaatttttcttatcaaatgagg--ccatgtcatagaggagattgctaatt---ttttgttctcatggtggcagGTGCATGTTCAATCAGATCCTGCTGGACGTATGGTTATCACAGGGGATCCAGAGCAGCCTGATGATCCTTGGGGGATCACTCTGTTCAAGAAG
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G421899_T01 (Zea mays), 3'ss of exon 10
gtgaaaaaatat-----ctttaatgttgaacgcatcacttcaaactgttccattttcctaaaataaatacctgacttaatttgtgcgtaacaaacaaaaagcttccacttcttgaactgaggcactacctgcgagaagaaatgaattgttgaattttgttctaaatggtgcagGTGCATGTTCAGTCAGATCCTGCTGGGCGTCTGGTTATAACTGGGGACCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCATTCAAGAAG---
|||| || ||| | ||| ||| || || | || ||| || |||| | |||||||||| | | | || || | || ||||| | | | | || |||||| | || ||| ||||| | || ||| ||||| | | ||||||||||||||| |||||||||||||| ||||||||||| || ||||| ||||||||||||||||||||||||| ||||||||| |||||||||
gtgaggaagtatggtgccattattgtggacagcgtagttttaaatattttcattgacataaaataaatcctttaggagataaatggaagataagcaaaatgaatttttcttatcaaatgaggccatgcca--tagaggaaattgctaatt---tttcgttctcatggtggcagGTGCATGTTCAATCAGATCCTGCTGGACGTCTGGTTATCACAGGGGATCCAGAGCAGCCTGATAATCCTTGGGAGATCACTCCGTTCAAGAAGGTG
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G421899_T03 (Zea mays), 3'ss of exon 9
gtgaaaaaatat-----ctttaatgttgaacgcatcacttcaaactgttccattttcctaaaataaatacctgacttaatttgtgcgtaacaaacaaaaagcttccacttcttgaactgaggcactacctgcgagaagaaatgaattgttgaattttgttctaaatggtgcagGTGCATGTTCAGTCAGATCCTGCTGGGCGTCTGGTTATAACTGGGGACCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCATTCAAGAAG
|||| || ||| | ||| ||| || || | || ||| || |||| | |||||||||| | | | || || | || ||||| | | | | || |||||| | || ||| ||||| | || ||| ||||| | | ||||||||||||||| |||||||||||||| ||||||||||| || ||||| ||||||||||||||||||||||||| ||||||||| |||||||||
gtgaggaagtatggtgccattattgtggacagcgtagttttaaatattttcattgacataaaataaatcctttaggagataaatggaagataagcaaaatgaatttttcttatcaaatgaggccatgcca--tagaggaaattgctaatt---tttcgttctcatggtggcagGTGCATGTTCAATCAGATCCTGCTGGACGTCTGGTTATCACAGGGGATCCAGAGCAGCCTGATAATCCTTGGGAGATCACTCCGTTCAAGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaggcactacctgcgagaagaaatgaattgttgaattttgttctaaatggtgcagGTGCATGTTCAGTCAGATCCTGCTGGGCGTCTGGTTATAACTGGGGACCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCATTCAAGAAG
ttctaaa putative branch site (score: 2)
aattttgttctaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaaaaatatctttaatgttgaacgcatcacttcaaactgttccattttcctaaaataaatacctgacttaatttgtgcgtaacaaacaaaaagcttccacttcttgaactgaggcactacctgcgagaagaaatgaattgttgaattttgttctaaatggtgcagGTGCATGTTCAGTCAGATCCTGCTGGGCGTCTGGTTATAACTGGGGACCCAGAGCAGCCTGATAATCCTTGGGGGATCACTCCATTCAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG