Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
Basic information
species | Oryza sativa |
transcript | LOC_Os11g01380.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G111355_T01 (Zea mays), 3'ss of exon 1
---------gtatgcaactcttccaattcagtgttattggagtatcatcattc-tcatgtgctatgtatttaaattcttattttcctttatat---tgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
||| | || | | || || | ||| | | || | || | || | | |||| ||| ||| || ||| | | ||||||| || || ||||||||||| || || || || ||||||||||||| |||||||||||||| || ||||||||||| || ||||| ||||||||||
gttcagaaggtagttgtgtgtttcgactctgt-taattcgtgcgtcgttcctcataataggttgagtatgagaatggttaattcttttttcttgtttccagGTGAATCCCGGGAATGCTCCATTGGTAGTGGGGCAATTACTTGATGATGAATGCCCTGAAGATTTTATCAAGGGTTTGATCCTCTCTGTTCGTTCTCTCC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 19
gtatgcaactcttccaattcagtgttattg-gagtatcatcattc---tcatgtgctatgtatttaaattcttattttcctttatattgta----gGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
||||| | || | || ||| ||||||| | | |||| ||| | | | | | |||| | || ||| | ||| | ||||| ||| || ||||| |||||||| || || ||||| || || || |||||||| ||||| ||||||||||| |||||||||||||| ||||| |||||||| |
gtatgtacatccttgaagtcactgttattttgggcgtcattcttcatctggtatttcaagcatttgtttgattgtttccttttgtcttgtatgtagGTCAATCCTGGTAATGCTCCCTTGGTAGTTGGGCAACTTCTGGATGATGAATGCCCGGAAGATTTCATCAAGGGTTTGATTCTCTCTGTTCGTTCTCTGC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA11G06720.1 (Glycine max), 3'ss of exon 21
---------------------gtatgcaactcttccaattca-gtgttatt--ggagtatcatcattctcatgtgctatgtatttaaattcttatttt---------cctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
|||| | | || || | || || || || | | || || | || ||| |||||| | | | | | || ||||| || |||||||||||||| ||||||| |||||| | | |||||||| |||||||||||||| || || ||| | || || || || || |||||||
gtaaatttgttttcagggtttgtatttgatttttgtgatccttgtagcatgtaggtgtgctttaaatcattcttgaaaagttttttaattctgacctaaactttgaacttcttgcttttagGTCAATCCTGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAAGATTTTATCAAAGGTCTTATACTTTCAGTTCGCTCTCTCC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 20
--------gtatgcaactcttccaattcagtgtta-ttggagtatcatcattctc-atgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
|| |||| | | | | || || | | | | || | | || || | ||| | | || | || ||||||||||| || |||||||| ||||| ||||| ||||| | |||||||| ||||| |||||||| || || || |||||||| ||||| ||||| | |
gtattatagtttgcattaataatgctgtaatcttgcttattacacaaatactatctactttctctgccccactcataacattgtgccttct-ttatagGTGAACCCAGGGAATGCTCCTTTAGTCGTTGGGCAGCTTTTAGATGATGAATGCCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTAC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 21
gtatgcaactcttccaattcagtgttattggagtatcatc-attctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
|||| | | | | | | | || |||| ||| | ||| | || ||| |||| | | | |||| |||||||||| || ||||| || ||||||||||| ||||| || |||||||| ||| | |||||||| || || || ||||| || ||||| ||||| | |
gtataatagtagccttgctta-tctcat--gagtgctatctactctttttctctgcctatgtaaaacttcgtgcctttctata---cagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAATGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 19
--------------------------gtatgcaactcttccaattcagtgttattggagtatcatc---attctcatgtgct-atgt---atttaaattctt---attttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
|||| || | || |||| | |||||||| | | || | | ||| || | | | |||| | || ||||| | | |||||||| || ||||||||||| ||||||||||||| || | |||||||| |||||||||||||||||||| ||| | || || || || |||||||| |
gtatttgttgtgacttgtaaagtgtggtatttaatttttatgattc----tcattggagtgtatttcaaatctttctacgctgatatcaaacatgaatttcttatgttatccttcttgctatagGTGAATCCAGGAAATGCTCCTCTAGTTGTTGGACAATTATTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTTATACTTTCAGTTCGTTCTCTTC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 21
-------------------gtatgcaactcttccaattcagtgttattggagtatc------atcattctcatgtgctatgtat--ttaaattcttatttt--cctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
|||| || | || |||| ||| ||||| | ||| ||| || ||| | | || ||||||| || |||| | | |||||||| || ||||||||||| ||||||| |||||| | | |||||||| |||||||| ||||||||||| ||| | ||||| || || |||||||| |
gtatttgttgtgacgggtggtatttaatttttatgattct-caatataggagtgtattttaaatctttccaggctgatatcaaacatgaatttcttatgttatccttcttgctttagGTGAATCCAGGAAATGCTCCTCTAGTTGTAGGACAGTTGTTAGATGATGAATGCCCTGAGGATTTCATTAAAGGTCTTATTCTTTCAGTTCGTTCTCTTC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 20
--------------gtatgcaactcttccaattcagtgtt-attggagtatcatcattctcatgtgctatgtatttaaattcttattttc--ctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
| || || | | | || | || || ||| | | | | | | | | ||| | || | || ||||||||||| || |||||||| ||||| ||||| ||||| | |||||||| || || |||||||| || || || |||||||| ||||| ||||| | |
gtattatagtttgcattaataatgctgtaaccttgctttttacatgaatactatctagtatctactttctctgccccactcataactttgtgccttgttttatagGTGAACCCAGGGAATGCTCCTTTAGTCGTTGGGCAGCTTTTAGATGATGAATGTCCAGAAGATTTTATCAAAGGCTTGATTCTCTCTGTTCGTTCCTTAC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GLYMA02G42560.1 (Glycine max), 3'ss of exon 21
gtatgcaactcttccaattcagtgttattggagtatcatc-attctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
|||| | | | | | | || || | ||| | ||| | || ||| |||| || | | |||| |||||||||| || ||||| || ||||||||||| ||||| || |||||||||||| | |||||||| || || || ||||| || ||||| ||||| | |
gtataatagtagctttgctta-tctcat--gattgctatctactctttttctctgcctatctaaaactttgtgcctttctata---cagGTGAACCCAGGGAATGCACCTTTAGTTGTTGGGCAGCTGCTAGATGATGAGTGCGCAGAAGATTTTATCAAAGGCTTGATCCTTTCTGTTCGTTCATTAC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 21
gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
||||| | | | | ||||| | | ||| ||||| | ||| || | ||| || ||||||||||| ||||| |||||||| |||||||| || ||| | |||||||| || |||||||||||||| || || || | ||||| ||||| ||||| | |
gtatgtagtttctttagacttttgtta--aatatggtaggattttcatgaaagaattatata------tgcgatccctt---ttgtagGTGAATCCTGGGAATGCTCCCTTAGTTGTGGGGCAGTTGCTTGATGACGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTTTCTGTTCGTTCATTAC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 21
gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
|||| | | | ||| || | | | | | |||| | | ||| || || || | | ||||||||||||| |||||||| |||||||| || ||| | ||||||||||| |||||||||||||| || || || | ||||| ||||| ||||| | |
gtataaggtttcctgggactacttttaatgcgttggagtt-cagtttttttttatgaa---atatttatacgtttgattctgtcaaagGTGAACCCTGGGAATGCTCCCTTAGTTGTCGGGCAGTTGCTTGATGATGAATGCCCTGAAGATTTTATAAAAGGCCTCATTCTCTCTGTTCGTTCATTGC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 21
---------------------------------------------gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatt-taaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
||| | | || || | | | | |||| | | ||| ||| | | ||| | ||| ||||| | ||||| || || ||||||||||| |||||||||| || || || |||||||| |||||||||||||||||||| ||| | ||||| || || || ||||| |
gtacaattactgtaaggagttatttatttatttatttatttttccaaatgaagatgtttca--ttattttaattgcactgagtccatgtctgcagaagatgaaccatgtattttcttttgtctttaattgatagGTAAATCCGGGAAATGCTCCTCTAGTTGTTGGGCAACTTCTAGATGATGAATGCCCTGAAGATTTCATTAAAGGTCTCATTCTTTCAGTTCGGTCTCTTC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 21
------------------------------------------------gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatttaaattc-ttattttcctttatattg-tagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
||| | || || | | | | | || | || | ||| | ||||||| || ||| || | ||| |||||||||||| | ||||| || |||||||| || ||||| || |||||||| || || |||||||||||||| ||| | ||||| |||||||| || || |
gtgtgagttccttctagaattctagaattttggatcccctttgggtcatgatgaactcctgtggatgcttcaatgccctaat-taattttagtcttcaattatttgattaaattaattgcttttgcttctcttgatagGTGAACCCTAGTAATGCACCTTTAGTTGTGGGGCAGCTGCTAGATGATGAATGTCCAGAAGATTTCATTAAAGGTCTAATTCTTTCTGTCCGGTCGCTGC
upper sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 21
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 21
-------------------------gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtattt----aaattcttattttcctttatatt----gtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
|| | || |||| | || || | | | |||| | || |||| | | || | | | ||| || | |||| || || ||| || || || ||||| || | ||||||||||| |||||||| || ||||||||||||||||| | || ||||| || || |
gtaatttgagattcaatgatacatggttcgtaagaattcctgtacaatgagtaaaaattgattctccttcaatgtagtttggatttcttgatgtctgtactgccttctatttttcatgcagGTCAATCCACAAAACGCACCTCAGGTGGTTGGGCAATTGCTTGATGATGATTGCCCTGAGGACTTCATTAAGGGTTTGATCTTATCCGTCCGCTCACTGCMapped 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|87006844|gb|CI285878.1|CI285878EST: ATCTGTATACAAATAATATGCTTCGGTATATTGAAGGCTATGTACAGAAA GTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAG
genomic: ATCTGTATACAAATAATATGCTTCGGTATATTGAAGGCTATGTACAGAAAgtatgcaact ... tatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAG
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
72 (upstream exon),
75 (downstream exon)
Score:
143GCTGATTAATGTCTGCGACCGCTTTGGATTTGTTCCAGATTTGACCCACTATCTGTATACAAATAATATGCTTCGGTATATTGAAGGCTATGTACAGAAAgtatgcaact ... tatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatcattctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
ttcttattttccttta CT-rich tract
tatgtatttaaattct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaactcttccaattcagtgttattggagtatcatcattctcatgtgctatgtatttaaattcttattttcctttatattgtagGTGAACCCTGGAAATGCTCCATTAGTTGTTGGACAGCTACTTGATGATGAGTGCCCTGAAGATTTCATTAAGGGTTTGATTCTGTCTGTCCGTTCTCTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA