Sequence
atgc intronic sequence ATGC exonic sequencegtcatgttgaatcttgttctcgacccacgataccttcacaacctacaatggtttcccatgttttgatgtgttgcctaacattacactgattggtgatgcatatcttatttcaacttttcagTTGGTTATCACAACGGTGGTCTTTGCCTAAAGGATAGGAGTGTCGTTGAGGGACTTTTCCTGAAGGGTGATATTCAAATTCTTTGCACGACGAATACTTT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g40450.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G346278_T01 (Zea mays), 3'ss of exon 7
----------------------------------------------------------gtcatgttgaatcttgttctcgacccac-gataccttcacaacctacaat-ggtttcccatgtt--ttgatgtgttgcctaacattacactgattggt-----gatgcatatcttatttcaacttttcagTTGGTTATCACAACGGTGGTCTTTGCCTAAAGGATAGGAGTGTCGTTGAGGGACTTTTCCTGAAGGGTGATATTCAAATTCTTTGCACGACGAATACTTT
| || | | ||| || || | ||| | | | | |||||||| ||||| | || || |||||| | |||||| ||| | || || ||||||||||||| ||| || |||||||||||| |||| || | || | |||||||| |||||||| ||||||||| ||||| |||| ||||| || ||||||||
gttatctggaatcttgttccctgggcacccataataccttccttaactttgcaagctccattttttcagtaatgtcttcttttttttgaaagggaagcaatgtctttttaggtgcccatgttagttgatacacttataaaactttagttgattgcttaacagatgca-atcctgttcca--ttttcagTTGGTTTTCATAATGGTGGTCTTTGCTTAAAAGACCGAGGTCTTGTTGAGGGGCTTTTCCTCAAGGGTGATCTTCAAGTTCTATGCACAACAAATACTTT
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G346278_T02 (Zea mays), 3'ss of exon 6
gtcatgttgaatcttgttctcgacccac-gataccttcacaacctacaat-ggtttcccatgtt--ttgatgtgttgcctaacattacactgattggt-----gatgcatatcttatttcaacttttcagTTGGTTATCACAACGGTGGTCTTTGCCTAAAGGATAGGAGTGTCGTTGAGGGACTTTTCCTGAAGGGTGATATTCAAATTCTTTGCACGACGAATACTTT
| || | | ||| || || | ||| | | | | |||||||| ||||| | || || |||||| | |||||| ||| | || || ||||||||||||| ||| || |||||||||||| |||| || | || | |||||||| |||||||| ||||||||| |||||
----ttttcagtaatgtcttcttttttttgaaagggaagcaatgtctttttaggtgcccatgttagttgatacacttataaaactttagttgattgcttaacagATGCA-ATCCTGTTCCA--TTTTCAGTTGGTTTTCATAATGGTGGTCTTTGCTTAAAAGACCGAGGTCTTGTTGAGGGGCTTTTCCTCAAGGGTGATCTTCAA-----------------------
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA16G07850.1 (Glycine max), 3'ss of exon 9
------------gtcatgt-tgaatcttgttctcgacccacgataccttcacaacctacaatggtt----tcccatgt-tttgatgtgttgcctaacattacactgattggtgatgcatatcttatttcaactttt-cagTTGGTTATCACAACGGTGGTCTTTGCCTAAAGGATAGGAGTGTCGTTGAGGGACTTTTCCTGAAGGGTGATATTCAAATTCTTTGCACGACGAATACTTT
|| | | ||| | | | | | | ||| | | | || || ||||||| ||| | | | ||| ||| |||| || || | | ||||||||||||||| ||||| |||||||| || ||| | ||| | || || || ||||| || |||||||| |||||| | |||||||| || |||||
gtatgaaaggaatctatatattgttctgggatttggctaaataataattcttactggaaagtgattgcaatcccatgcacctgaattagaatttcaaattg-gtagatatgtgacttttagaaaatggctttcctagTAGTTGGTTATCACAATGGTGGGCTTTGCCTCAAAGATCGAAGTATTGTGGAAGGCCTTTTTCTCAAGGGTGACATTCAAGTACTTTGCACTACAAATAC---
upper sequence: LOC_Os02g40450.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv14s0066g00880.t01 (Vitis vinifera), 3'ss of exon 9
gtcatgttgaatcttgttctcgac-ccacgataccttcacaacctacaatggtttcccatgttttgatgtgttgcctaacattacactgattggtgatgcatatcttatttcaacttttcagTTGGTTATCACAACGGTGGTCTTTGCCTAAAGGATAGGAGTGTCGTTGAGGGACTTTTCCTGAAGGGTGATATTCAAATTCTTTGCACGACGAATACTTT
|| || ||| || | ||| || | || || | || | ||| | |||| || || | | || ||| ||| | | | || | || | |||||||||||||| ||||| ||||| ||||||| ||||||| | | | || |||| || ||||| || |||||||| ||||||||||| || || || |||||| |
-----gtataagcttatttttcttaccataatgc-ttgttaatttgaaa-gtttttcaatgtccctat-tgct-cacaaagttagtttga--aatagtata-atttgatagcttgttttcagTTGGTTACCACAATGGTGGACTTTGCCCAAAGGATCGCAATCTCATTGAAGGTCTTTTTCTTAAGGGTGACATTCAAATTCTGTGTACCACAAATACTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgttgcctaacattacactgattggtgatgcatatcttatttcaacttttcagTTGGTTATCACAACGGTGGTCTTTGCCTAAAGGATAGGAGTGTCGTTGAGGGACTTTTCCTGAAGGGTGATATTCAAATTCTTTGCACGACGAATACTTT
cttttc CT-rich tract
atatcttatttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcatgttgaatcttgttctcgacccacgataccttcacaacctacaatggtttcccatgttttgatgtgttgcctaacattacactgattggtgatgcatatcttatttcaacttttcagTTGGTTATCACAACGGTGGTCTTTGCCTAAAGGATAGGAGTGTCGTTGAGGGACTTTTCCTGAAGGGTGATATTCAAATTCTTTGCACGACGAATACTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG