Sequence
atgc intronic sequence ATGC exonic sequencegtcagcttcacagctaaacatgtctgatactttgatgttactaatctctaaccttttttgtctgatgtacttgtaaaacccatttggtgatggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g57750.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g57750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G081965_T01 (Zea mays), 3'ss of exon 6
gtcagcttcacagctaaacatgtctgatactttgatgtta--ctaatctctaaccttttttgtctgatgtacttgtaaaacccatttggtgatggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
| | | | | |||| || | | | ||| | || | | | | | | || | ||| ||||| | ||||||| || ||| || |||||||||||||||||||| ||||||||||| ||||| | ||||| || ||||| ||||| || ||||| || || |||| ||||||||| ||
-gtgggtactccacatgacatttcaggttccttgtgcacaagctggtgtatgtgatgcgtgatttgtaatgctt--taaacctttcgggtgatgatggcagGTGTGGGCACATGTGTACTTGCTCGAAATGTGCAAATGAGCTGGTGCGCAGCGGCGGCAAGTGCCCGCTCTGCCGGGCTCCCATCGTGGAGGTGGTCCGC
upper sequence: LOC_Os02g57750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G34240.1 (Glycine max), 3'ss of exon 9
--------------------------gtcagcttcac-agctaaacatg-tctgatactttgatgt-tactaatctctaaccttt----tttgtctgatgtacttgtaaaacccatttggtgatggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
| || | | | ||| | | | | | | || | ||| | || | | || | | | | | || | ||| | | |||||| ||||||||||| ||||| ||||||||||| || ||| ||||||| ||||||| ||||| || |||||||||| || || |||||||| ||
gtatttatacattatactatatataatttgtgttgatgaacaaaatacaaccctacattataatatgcactgtttactttttctgaacactggttttgtttcttcctttctccaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTCTTGAGGTGGTCCGA
upper sequence: LOC_Os02g57750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G33300.1 (Glycine max), 3'ss of exon 8
-----------------------------------gtcagcttcacagctaaacatgtctgatactttgatgttactaatctcta------accttttttgtctgatgtacttgtaaaacccatttggtga--------tggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
| | | | | || | | | || | | | || | | || || | || || || |||| || || || | | | |||||| ||||||||||| ||||| ||||||||||| || ||| ||||||| ||||||| ||||| || |||||||||| || || | |||||||| ||
gtacttatacatgataaaatatataatttgtgttgatgaacaaaaaatacaaccctacattttatgcaggtatctgtagtttatactgtttacttattctgaacactggttttgtttcttcctttcggcaaattgcaatttcttgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCCAATGAGTTAATTCGTGGTGGTGGTAAATGTCCTTTATGCCGAGCACCAATTGTTGAGGTGGTCCGA
upper sequence: LOC_Os02g57750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: AT5G04460.3 (Arabidopsis thaliana), 3'ss of exon 7
gtcagcttcacagctaaacatgtctgatactttgatgttactaatctctaaccttttttgtctgatgtacttgtaaaacccatttggtgatggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
| | || | ||||| | | || || | | || ||| ||| || || | | |||||||||| ||||||||||||||||||||||||||||| ||||| | | | || || ||||| || || || |||| |||||| ||||| | ||
---------------gtaactaactaactctttgctcaaaaaaaaaattattgtctcttaaactcaaaactgaacaaatccttt-----aaaattacagATGCGGACACATGTGTACTTGCTCAAAATGTGCAAATGAGCTTGTAAGAAACGGAGGAAAATGTCCGCTTTGTAGAGCACCGATCATCGAGGTAATCCGA
upper sequence: LOC_Os02g57750.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv13s0019g05390.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------gtcagcttcacagctaaacatgtctgat--actttgatgttac----taatctc---taaccttttttgtctgatgtacttg-taaaacccatttggtgatggtg-acagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
| || | | ||| | ||| | ||| ||| |||| || | | ||| | | | | || | || || | || |||||| ||||||||||| ||||| |||||||||||||| ||| | |||| |||| || || |||||| | |||||||| ||||| | ||||| | ||
gtatatgcctgcttatttgtgctttttccctctgggatctatcttttttttttatcagaacctccgggatctatcttgggactaccttttaatttcgtgttgctgtttcttccccttatctttactgtcttccgttgaaaaaaaatgtgcagATGTGGGCACATGTGCACTTGTTCAAAATGTGCAAATGAGTTGGTTCGTGGTGGAGGAAAGTGCCCATTGTGCCGAGCCCCGATTGTTGAGGTCATCCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctctaaccttttttgtctgatgtacttgtaaaacccatttggtgatggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
ttttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagcttcacagctaaacatgtctgatactttgatgttactaatctctaaccttttttgtctgatgtacttgtaaaacccatttggtgatggtgacagATGCGGGCACATGTGTACTTGCTCAAAATGTGCAAACGAGCTAATTCGCAGTGGTGGCAAATGCCCACTATGCCGAGCGCCGATCGCGGAGGTGGTTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG