Sequence
atgc intronic sequence ATGC exonic sequence...cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
-----------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgctaata-atttatattgcagaa-gttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
| ||| | | || | || | |||| || ||| | || | |||| || | |||| ||||| |||||| ||| ||||||||||||||||||||||||||||||||||||||||||||||||||| || || |||||||| || |||||||| ||||||||| |||| | ||| || |||
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggct--gcataagattctctattctatactagtaatagaatgtcacaatat-cagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaa-acagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
| | || ||| | | | | | ||| || | ||| || || | || || | | | | | || | |||||||||||||||| ||||| ||||| ||| |||| || || ||||| |||||||| ||||| || || ||||| ||| | | |||| | |||||| |||
ttttgcatacaaagaaaagcatttttctggatcctattatatttattcat-ttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
-----------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgct------aataatttatattgcagaagttatta---tatgttttatga--gttaacaaagg---cctaaaa--acagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
| | | | | | || || | | | | | | ||| | || | | ||| || || ||| ||| | || | | | | | | |||||||||| |||| ||||||||||| |||||||| || || ||||| || ||||| |||||||| ||||| || || |||| | |||| | ||| || |||
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaa-atgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatcacagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 8
-------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgctaataat--ttatattgcag---aagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
| | || || ||| | || | | | || |||| | | | || || | |||| ||| | | | || | | |||| |||||||||| || ||| || |||||||| || |||||||| || ||||| ||||||||||||||||||||||||| | |||| | | || | |||
gtgagtgatcttttggtctttgtctagttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatgtggaattttaatttctgatattctttttaaatgctcatttgatcat--acagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatat-gctaataatttatattgcagaagttattatatgttttatgagttaacaaagg--cctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
| | || || | | | ||| | | ||| | || | | | | | | || ||| | | | | | | ||| ||||||||||| || |||||||| |||||||| || || ||||| || ||||| |||||||| || || || ||||| | | |||| | || ||| ||
-tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttatttag--tgctctttcctggatcagtcagtgatagtacttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S301_53V6.1 (Physcomitrella patens), 3'ss of exon 8
cctagacaactaaggc--tgtagcctatgtata-acatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
|| | |||| | | ||| | | | | | | | || | | | |||| ||| | | || || | || ||| |||||||| ||| | |||||| | || || || || ||||| |||||||| |||||||||||||| |||||| |||| |||| || |||||
gatatattactaggatgatttagaatttttctgtatccagaatgatcttaccaagtttgcaagtacttaagggacagtcgtattgttaatga---gaattcagGTTTGAGGAGACTGAGCCTCCTGGAGCTAGGTCGTTTTTCACAGAGATTATTGCTTCAATTTCTGATATCAAGTTTGCAAGAGGTGGCCGGTACATTCTG
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S167_51V6.1 (Physcomitrella patens), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcct-----aaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
| || | ||| | | ||| | ||| || | || | | | | | | | | | | | | | ||| |||||||| ||| |||||||||||||||| ||||||||||| || || || ||||||||||| |||||| | || || || |||||
-----tgcgtttttcctaaaagttatatttccacaatggttataggttgtgttttctgaatattggtttcatattgaaacttgtattgtctttttgtgggtgcagGTTTGAGGAGACTGAGCATGCTGGATCAAGATCCTTTTTTACAGAAATCATAGCTTCTATTTCTGATATTAAGTTTGCGAGAGGCGGTCGGTACATTCTG
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 8
-cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgtttta--tgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
|| |||| | | | | | | || ||| | || | | || | || | || | ||| | | | | | | ||| |||||||| ||| | |||||||||| || || || |||||||| ||||| ||||||||||| || |||||| |||| || ||||||||
gttgagggaactgatcattcactggttatgtccca-atgttgatg-tatgtac-gaggatatgctttttcgttgaagtttgcatggtattgatgtggttgcagGTTTGAGGAGACTGATCCCTCTGGATCAAGGTCTTTTTTCACAGAAATCATTGCTTCAATTTCTGACATTAAGTTTGCAAGAGGTGATCGGTATATTCTC
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaa-----ggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
||| | | | | || | | | | | | | | || ||| | || || | | | | | | | || | | | ||| |||||||| |||| | ||||| | || || || || |||||||||||||| ||||||||||| || |||||| |||| ||| || |||||
--aagatatttctaga-atggcttggaagtttccactaccta-gagtgatcttg-ataaattttcttgtagtaaaaggacaaccatattcggaacttgtgtgcagGTTTGAGGAGAATGAGCCTGCTGGAGCGAGGTCGTTTTTCACAGAAATTATTGCTTCAATTTCTGACATCAAGTTTGCAAGAGGTGGTCGGTACATTCTA
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
|| || | | || | |||| | | || || || |||||||| ||||| |||| | ||||||| || |||||||||||| |||| || || || ||||| |||||||| | | ||| || |||||
----------------------------------------------gtaagttcttgtcttctacgcctggactg-aagtt--ccatccttccaatgtagGTTCGAGGAACAGGAAGCTCCTGCAACAAGATCATTTTTTACAGAAATTGTTGCCTCCATCTCGGATATCAAGTTTTCTCGTAGTGGACGGTACATTCTC
upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 8
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
|| || | | || || ||| | || | || || || |||||||| ||||| |||| | ||||||| || |||||||||||| |||| || || || ||||| |||||||| | | ||| || |||||
----------------------------------------------gtaagttcttg--tcttctacgcgtggactgaagttccatccttccaatg-tagGTTCGAGGAACAGGAAGCTCCTGCAACAAGATCATTTTTTACAGAAATTGTTGCCTCCATCTCGGATATCAAGTTTTCTCGTAGTGGACGGTACATTCTCMapped 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|31352864|gb|CD437221.1|CD437221EST: CGACTTATTGATCTGCGCCAATCAGCACTGTGTGACAACCATTCAAAAAT ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST:
gi|211384024|gb|FL015619.1|FL015619EST: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST:
gi|24934206|gb|CA452424.1|CA452424EST: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST:
gi|211386654|gb|FL015627.1|FL015627EST: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST:
gi|211386649|gb|FL015622.1|FL015622EST: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
EST:
gi|67025874|gb|CO454623.1|CO454623EST: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAAT ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
genomic: CGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTAT
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:
168ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
Block sizes:
49 (upstream exon),
47 (downstream exon)
Score:
152ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
168ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
167ATCCATCCCATTGTAATACACTGGCCTATAGTAGTTCAAAGGGTTCTATCCGACTTATTGATCTGCGTCAATCAGCACTGTGTGACAACCATTCAAAAATgttagtaacc ... ctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
gcctaaa putative branch site (score: 167)
ttattatatgttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctagacaactaaggctgtagcctatgtataacatatgctaataatttatattgcagaagttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA