Sequence
atgc intronic sequence ATGC exonic sequencegtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g51430.1 (Oryza sativa), 3'ss of exon 10
---------gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
|| | | | ||||| || |||||| | || | || ||| | ||| |||| | | |||| ||| || ||||| |||||||| || || || || || |||||| | |||||||| || |||||||||||||||||||| ||||||||||||||||| || |
gtaagttttgtggaaatttattctagacttctggtaattggtgatctcattgtttaagctaagttggttatgctggtgtgcttctcaaa--gGTAGCTCGTGGTGACAAGACTGATGAAGACGGCGTCCCCATGTTACTAAAAATTCCACGAATGTTTGATCCATGGGGAGGATACAGCATCATTGGATTCG
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA01G42940.1 (Glycine max), 3'ss of exon 10
----gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaat-tttgctggttatagcatg--ttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
||| || | | || | | | | ||| | ||| || || || | || ||| | || |||||| || || ||||| | | || ||||| | |||||| | || || |||| || || ||||||||||||||||| ||||||||||| || ||||
gttagtatatgttctattctaattcatgacaatcactatcaccctatgtatttactaattttaattttgcttactttttactcaccatagGTGGCCCGAGGCGATCGAAGTGGAGAAGATGGAATTCCCATGTTACTGAAGTTCCCTCGGATTTTTGATCCATGGGGTGGTTACAGCATCATAGGTTTTG
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA18G46760.1 (Glycine max), 3'ss of exon 10
------------------------------gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggtta---tagcatgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
| | || | | | ||| | | | ||| || ||| || |||| | |||| || || || || | || | || |||||| | || ||||| || || || || || ||||||||||| |||||||| |||||||||||||| ||||
gtgagtgatttcgaggaagatctcccttagactattcttcacaaagcttgttttttatctcataaaacatgatgcttttcttattaaactaatgcaacattttcacttctttgcagGTAGCTCGAGGTGATAGGAGTGGAGAAGATGGTATCCCTATGCTACTCAAGATACCACGTATGTTTGATCCCTGGGGTGGTTACAGCATCATTGGTTTTG
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA11G02540.1 (Glycine max), 3'ss of exon 10
gtaagcgtg----tgaaaggggattc-tgctatttggtggtatcctgaat-tttgctggttatagcatgt--tggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
|| || | | | |||| || | | | | ||| | ||| || || || | | | ||| | || |||||| || || || || | | || ||||| | |||||| | || || |||| || || ||||||||||||||||| ||||||||||| || ||||
gttagtattatgctctattctaattcatgacaatcactatcaccctatgtatttactaattttaatttttcttactttttactcaccatagGTAGCCCGAGGTGATCGAAGTGGAGAAGATGGAATTCCCATGTTACTGAAGTTCCCTCGTATTTTTGATCCATGGGGTGGTTACAGCATCATAGGTTTTG
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA09G39500.1 (Glycine max), 3'ss of exon 10
------------------------------gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaat--tttgctggtta---tagcatgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
|| || | || || | | || | || ||| || ||| || |||| | |||| || || || || | || | || |||||| | || ||||| || || || || || ||||||||||| |||||||| |||||||||||||| ||||
gtgagtgatttcttggaagatctcccttcgacaatatcacaaagcttgtttttgatctcataatacatgattgatgcttttcttattaaactaatgcaacattttcacttctttgcagGTAGCTCGAGGTGATAGGAGTGGAGAAGATGGTATCCCTATGCTACTCAAGATACCACGTATGTTTGATCCTTGGGGTGGTTACAGCATCATTGGTTTTG
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: AT1G01650.1 (Arabidopsis thaliana), 3'ss of exon 10
---------------------------------------------gtaagcgtgtgaaaggggattctgctatttggtggtatc---ctgaattttgctggttatagcatgttggtttc-----ttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
|| || | || | ||| || | | |||| || | | || | | || || | | | || |||||| || ||||| |||| | || ||||| || | || ||||| ||||| ||||| |||||||||||||| |||||||| |||||||| ||||| ||||
gtaagtttttcttttttgctccagaccatcatgcaagaagactttgttagatattccaactacacatacttatctgtctgctccacactgatattatcggagaattgtacgtcttttcccattttcccacatatagGTAGCCCGTGGTGACAGAAGCGGAGAGGACGGAATTCCAATGCTACTAAAGATCCCACGAATGTTTGATCCTTGGGGTGGCTACAGCATAATTGGATTTG
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv02s0025g03400.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
| | || | | | ||| || | | | | ||| | || | ||||| | | | |||||| || ||||| || | | | |||||||| | || ||||| || || ||||| || |||||||||||||||||||| ||||| |||||||||||||
gtaagtactgcttttttcacccatatgctagaccatggttattgtggttcaaataatgtgcagactttcaaatactaaaaagcattataaattggtcatgtttttatatagGTAGCTCGTGGTGATAGAAGTGGACAGGATGGTATTCCTATGCTACTGAAGATCCCCCGCATGTTTGATCCATGGGGTGGTTACAGTATCATTGGCTTTG
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 3'ss of exon 10
----------------------gtaagcgtgtgaaaggg---gattctgctatttggtggtatcctgaattt-tgctg----gttatag---catgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
|| ||| || || | ||| | ||||| || | ||||| ||| || |||| | | || | |||||| || ||||| || | || | ||||||||| | || ||||| || || |||||||||||||||||||| |||||||| |||||||||||||| ||||
gtaagtagtttctccaaaacttgttagcccaccaatacatttgaaacggctgatgtttggtacttgagatctctgctgcccaattacagaattatgtaattgtgttttctgtatagGTAGCTCGTGGTGATAGGAGTGGGGAGGATGGTATTCCGATGCTACTGAAGATCCCGCGAATGTTTGATCCTTGGGGTGGCTACAGCATCATTGGATTTG
upper sequence: GRMZM2G165351_T03 (Zea mays), 3'ss of exon 8
lower sequence: PP1S124_16V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------------------------------------------------------------gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtt----tcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
| | | | || | | || | | |||||| | | | ||| | || | ||||| | ||||||| || || || |||||| | | || ||| | || ||||| || ||| | || || | ||||||||||||||||| ||||| |||||||| ||||
gtatgttcatcaatctggcttttcctatttaagacgcgcgtttttgaaattgtttcgacttctaggttgtgaactattgagtgctttgacaaatgtcgtctttttcatcacttcaagctgacgatcggtagcttg-ggtatcacaatacacaagtgctgagatatgacgattgaacttttctg-ggacagGTTGCTCGGGGAGATAAGACCAATGGAGAGGGTATTCCTATGCTTCTTAAAGTTCCACGTCTTTTTGATCCATGGGGTGGCTACAGTATCATTGGTTTTGMapped 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|67025992|gb|CO454741.1|CO454741EST: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
EST:
gi|149073466|gb|EE161770.2|EE161770EST: CAAGAGATGGTTTCATGAGAGCGTGATGATTGTG G-TGCCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAA
genomic: CAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTG-CGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAA
EST:
gi|149086581|gb|EE176124.2|EE176124EST: AAGAGATGGTTTCATGAGAGCGTGATGATTGTG GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: AAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
EST:
gi|91054682|gb|EB165100.1|EB165100EST: AAGAGATGGTTTCATGAGAGCGTGATGATTGTG GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: AAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
EST:
gi|32843028|gb|CD982709.1|CD982709EST: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
EST:
gi|74234147|gb|DT642061.1|DT642061EST: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
EST:
gi|67024697|gb|CO453446.1|CO453446EST: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
EST:
gi|32848049|gb|CD987730.1|CD987730EST: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
EST:
gi|67017568|gb|CO446317.1|CO446317EST: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTG GTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
genomic: TCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAA
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 4 RNA-Seq libraries.
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
194GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
188GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
183GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
174GTGGGTTCGGTTCTTCTCGGCTGTGCCTTCCTGTATGATATCTTCTGGGTGTTTATCTCCAAGAGATGGTTTCATGAGAGCGTGATGATTGTGgtaagcgtgt ... ctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
tttcttctgc CT-rich tract
tgaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcgtgtgaaaggggattctgctatttggtggtatcctgaattttgctggttatagcatgttggtttcttctgcaaatagGTTGCGCGTGGCGACAAGACCGACGAGGATGGTGTGCCCATGCTGCTAAAAATCCCGCGAATGTTTGATCCATGGGGTGGATACAGCATCATTGGCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA