Sequence
atgc intronic sequence ATGC exonic sequencegtcagtcagtgttgacttggctcagcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
Basic information
species | Oryza sativa |
transcript | LOC_Os01g42650.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G064753_T01 (Zea mays), 3'ss of exon 4
-------------gtcagtcagtgttgacttggctcagcgaaaactctaaactg--------ccaaatatt-atgcaata------ctggtatcaacattttttcactt-ctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
||| || || || | | ||| | | ||| | || ||| || || |||| | | ||| | | | |||| | |||||||||| || |||||||||||||||||||||||||||||||| ||||||||||| |||||||| || ||||| ||||||
gtaagccagtgttgtctatcgcccttatatttttttttctaaagttaacagctggtgtggtgcgaagcatttgtgtaaccaattgcttggtttttgcctttacttgcctgctttttctcccagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G134738_T02 (Zea mays), 3'ss of exon 4
gtcagtcagtgttg---acttggctcagcgaaaactctaaactgccaaa-tattatgcaatactggtatcaacatttt--ttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
|| |||| || ||| | || || | |||| | || ||| || | || || | | |||| | | | || ||| ||||||| || |||||||||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||
gtaagtcggtattgtttatttttctaaaataaaaatagctggtgtcaacctagtgtgtaagaaattgcttggttttttaactagcctactttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTT---
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G477366_T01 (Zea mays), 3'ss of exon 3
-------------gtcagtcagtgttg-acttggctc---agcgaaaactc--taaactgccaaatatt-atgcaa-----tactgg--tatcaacattttttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
||| || || | || || || || | | | ||| || ||| || || | || | | | || || || || ||| | |||||||||| || |||||||||||||||||||||||||||||||| ||||||||||| |||||||| || ||||| ||||||
gtaagccagtgttgtctctcgcccttatatttttttctaaagttaacatttggtgtggtgcgaagcatttgtgtaaccaattgcttggtttttgactttacttgcctgttttttctcgcagAGGATGAACACGATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G134738_T01 (Zea mays), 3'ss of exon 4
gtcagtcagtgttg---acttggctcagcgaaaactctaaactgccaaa-tattatgcaatactggtatcaacatttt--ttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
|| |||| || ||| | || || | |||| | || ||| || | || || | | |||| | | | || ||| ||||||| || |||||||||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| ||||||
gtaagtcggtattgtttatttttctaaaataaaaatagctggtgtcaacctagtgtgtaagaaattgcttggttttttaactagcctactttattggcagAGGACGAACATGATGTTGTATGGTTCTGGTTGAAAAAAGACGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AC215864.3_FGT010 (Zea mays), 3'ss of exon 2
-------------gtcagtcagtgttg-acttggctc---agcgaaaactc--taaactgccaaatatt-atgcaa-----tactgg--tatcaacattttttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
||| || || | || || || || | | ||| || ||| || || | || | | | || || || || ||| | |||||||||| || ||||||||||||||||||||||||||||||| ||||||||||| |||||||| || ||||| ||||||
gtaagccagtgttgtctctcgcccttatatttttttctaaagttaacagctggtgtggtgcgaagcatttgtgtaaccaattgcttggtttttgactttacttgcctgttttttctcgcagAGGATGAACACTATGTTGTATGGTTCTGGTTGAAAAAAGATGAGCCGCATGAGTGTCCAGTCTGCTCGCAATACTTTGTG
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G03680.2 (Glycine max), 3'ss of exon 4
--------------------------gtcagtcagtgttgacttggctc--agcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttt-----------tcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
|| | | ||| |||| | | | | | | ||| | | ||| ||||| ||| | |||| ||| ||||||||||||||||||||||||| ||||| ||| || | ||||| | || ||||| || ||||| || |||| ||||||||
gtggtgagtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G03680.3 (Glycine max), 3'ss of exon 4
-------------------gtcagtcagtgttgacttggctc--agcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttt-----------tcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
|| | | ||| |||| | | | | | | ||| | | ||| ||||| ||| | |||| ||| ||||||||||||||||||||||||| ||||| ||| || | ||||| | || ||||| || ||||| || |||| ||||||||
gtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagagGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G03680.1 (Glycine max), 3'ss of exon 4
-----------------------gtcagtcagtgttgacttggctc--agcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttt-----------tcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
|| | | ||| |||| | | | | | | ||| | | ||| ||||| ||| | |||| ||| ||||||||||||||||||||||||| ||||| ||| || | ||||| | || ||||| || ||||| || |||| ||||||||
gtgagtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTT
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA07G03680.4 (Glycine max), 3'ss of exon 4
-----------------------gtcagtcagtgttgacttggctc--agcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttt-----------tcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG--------------------
|| | | ||| |||| | | | | | | ||| | | ||| ||||| ||| | |||| ||| ||||||||||||||||||||||||| ||||| ||| || | ||||| | || ||||| || ||||| || |||| ||||||||
gtgagtatcagaatattccttgtttctcttaatgtcttcttgcatgtgaacttcttcccaaggtgatgaaaaaagctagaattctggttatggtgtttatgagggggtgaacaacttgttttgattacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGACAAGCCCCATGAATGTCCAGTGTGCGCACAGTATTTTGTTGTAAGTTCATAATGACTTTT
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G80230.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcagtcagtgttgacttggctca---gcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
|| ||| | || ||| | | | | | | || || || | | || | || | ||| ||| | |||||||||||||||||||||||| ||||| ||| || | |||| | | ||| ||||| || ||| |||| || || |
gtgggtcttttttattttgctttcattgtgtgcatcatgatttggtttatttttagtag-accaaaggagatatgatggtttttcattc-tctacagAGGATGAGCATGATGTTGTCTGGTTTTGGCTGGAGAAAGGCAAGTCTTTTGAATGCCCTGTGTGTACACAGTACTTCAAG
upper sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g05100.t01 (Vitis vinifera), 3'ss of exon 4
---------------gtcagtcagtgttgacttggctcagcgaa--aactctaaactgccaaatattatgcaatactggtatcaacattttt---tcacttctt-tcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
|| | || | || | | || || ||| || | || || | | || || | || | | | || | ||||||||| |||||||||||||| || ||||| |||||| | ||||| |||| |||| |||||||||||||| ||| |||| |
gtaagaccctcttttgtattcttttcttaattttgtcccttcaactaattctttcatga-atatgtttgatagtgtgataattaattgtcttatgttattgattataatttacagAAGATGAGCATGATGTAGTGTGGTTTTGGTTGCACAAAGACCAACCACATGTCTGCCCAGTCTGTTCTCAACATTTCAAGMapped 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|88518836|gb|CI445682.1|CI445682EST: GATAGTTGTGTT-TCGTGGTGGTGAAGGAG AGGATGAGCATGATGTTGTATGGTTCTGGTT-ANAAAAAGATGAACCGCAT
genomic: GATAGTTG-GTTGTCCTGGTGGTGAAGGAGgtcagtcagt ... tcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGA-AAAAAGATGAACCGCAT
EST:
gi|33797913|gb|CF324816.1|CF324816EST: TGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAG AGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATG
genomic: TGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAGgtcagtcagt ... tcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATG
EST:
gi|29646177|gb|CB651184.1|CB651184EST: TGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAG AGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATG
genomic: TGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAGgtcagtcagt ... tcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATG
EST:
gi|8335467|gb|BE040401.1|BE040401EST: TGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAG AGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATG
genomic: TGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAGgtcagtcagt ... tcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATG
EST:
gi|5005118|gb|AU069902.1|AU069902EST: TGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAG AGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATG
genomic: TGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAGgtcagtcagt ... tcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATG
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:
67 (upstream exon),
73 (downstream exon)
Score:
47GAGGCCCCAGCTGTCATTGAATCCTACTATAACAAGAGGATAGTTGGTTGTCCTGGTGGTGAAGGAGgtcagtcagt ... tcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgccaaatattatgcaatactggtatcaacattttttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
cattttttcacttctt CT-rich tract
aatattatgcaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtcagtgttgacttggctcagcgaaaactctaaactgccaaatattatgcaatactggtatcaacattttttcacttctttcatttacagAGGATGAGCATGATGTTGTATGGTTCTGGTTGAAAAAAGATGAACCGCATGAGTGCCCAGTCTGTTCACAATATTTTGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG