Sequence
atgc intronic sequence ATGC exonic sequence...accattatattttttttttaataaaagcaactgtttgcatactgaagatcaaactttccatactgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 21
---------------------------------------------accattatattttttttttaataaaagc-aactgtttgcatactgaagatcaaactt----tccatactgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
| | || || | || || ||| || | || | |||| | | | | || | || || | || | | ||| ||||||||||||||||||||||| || |||||||||||||| || || |||||||| || |||||||| ||||||| || || ||||||||| |||||||||| ||
gtaagcaagtgtttcaattgagtatacatgattaataaattgttaattagtacataaatcttcaccaaacagctaatttcttatgtggtgaatggtgagttgagaactgaagattattggctgatcat-tattattgactgtccaaccagATTATGATAGAATTATCAAGAATATTGAAAGGGGAGAGGCCAGGATATCACGGAAGGATGAAATTATGAGAGCCATCGGGAAGAAGTTAGACCGCTATAA
upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 21
-------------------------------------------------------------------accattatattttttttttaataa--aagcaactgtttgcatactgaa--gatcaaactttccatactga---tggattgtgtatgttttg-atcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
|| | |||| || | | || || | || || ||| |||| || || | |||| | || ||| || | | || | | | | |||||||||| || |||| || || ||||| | || ||||||||||||| ||| ||||||||||||||||| ||||||||||| |||||||||||||| ||
gtatattttgtaaccttttctcttactgtttgtattccctactgatgacctatttaatgtgtagctgactttgttattaacttgtaaccaagtaatggattgcttacatgctgagctgagtaatggtcagatacaaaatctgttttgactaaatatgatgtcctcatcctatcagATTATGACCGAGTTATTAAGAACATTGAGAAAGGAGAAGCAAGGATATACCGGAAGGATGAGATTATGAAAGCTATTGGGAAAAAGCTAGACCGCTATAA
upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA07G38050.1 (Glycine max), 3'ss of exon 21
accattatattttttttttaataaaagcaactgtttgcata-ctgaagatcaaactttccata--ctgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
| || | | || || ||| || | || | || || | || | ||| |||| ||| | |||||| || ||||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||| || |||||||| ||||| ||||||||||||||| | |||||||||||
-gtttgatgtgtgttgatttgccaaatgaagcttgaatttagttttccattaagatatcaagggtctgtctgatt-tgtgtactttgatttatg-gtttgcagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAA
upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 21
accattatattttttttttaataaaagc-aactgtttgcatactgaagatcaaactttccata--ctgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
| |||| ||| || | | | || || ||| | | | ||| |||| ||| | |||| | || |||||||||||||||||| ||||| |||||||| ||||| ||||| |||||||| || |||||||| ||||| ||||||||||||||| | ||||||||||
-ttaaaatatcaagggtttgatgtgtgttgatttgccaaatggcttgaattaaaatataaagggtctgtctgatt-tgtgtactttggtttatg-gtttgtagATTATGATAGAATTATTAAAAACATTGAAAGAGGGGAGGCAAGAATATCCCGGAAAGATGAGATCATGAAAGCTATTGGGAAGAAGTTGGACCGCTACAG
upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 21
-----accattatattttt--tttttaataaaagcaactgtttgcatactgaagatcaaactttccatactgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
| || | ||| ||||| | || | | | || || | | | || ||| || || | ||| || |||| |||||||| |||||||||| |||||||| ||||| |||||||||||||| ||||| || || || || |||||||| |||||||||||||| |||||| | |||||||||||
gataaggctttgttgctttaattttttctggaaattagtttctgtttag-aatgtttcaaggttctgc-ctaattg---gtgcattttttaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAGGCTATTGGAAAGAAGTTGGACCGCTACAA
upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 21
----------accattatattttttttttaataaaagcaactgtttgcatactgaagatcaaactttccatactgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
| || | || |||| | || ||| | || || ||| |||| || | | | ||||| || ||| |||||||| |||||||||| |||||||| ||||| |||||||||||||| ||||| || || || || |||||||| ||||| |||||||| |||||| | |||||||||||
agtgggataaggctttgttattaactttttttggaaattactttctgttta--gaatgtcaaggttc---tgcc--taatttgtgcat-tttgaatcattgtctg--cagATTATGACAGAATTATTAAAAACATTGAAAGGGGGGAGGCAAGAATTTCTCGGAAAGATGAGATCATGAAAGCTATTGGAAAGAAGTTGGACCGCTACAA
upper sequence: GRMZM2G010085_T02 (Zea mays), 3'ss of exon 13
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 21
accattatatttt--ttttttaataaaagcaac---tgtttgca-tactgaagatcaaactttccatactga-tggattgtgtatgtt-ttgatcattgtacaacc---agATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
| || ||| || || | |||| || |||||||| | | | | | | || || | | | || | || || | ||||| || |||||| || ||||| || || |||||||| || ||||||||||| || || | || ||||| || ||||| |||||||||||||| || || |||||||
gttagtaactttagattgttaagtaaagttaatgagtgtttgcagtgcgacaaagttggatatttatcctaagtaagctctgcctcttgttttcctttgtaaaaattgtagATTACGACAGAATCATCAAGAATATTGAGAGAGGGGAAGCAAGAATCTCTAGGAAAGATGAAATCATGAAAGCTATTGGGAAGAAACTGGATCGCTACAGMapped 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|67013537|gb|CO442286.1|CO442286EST: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCC
genomic: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCC
EST:
gi|6194488|gb|AW146592.1|AW146592EST: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATAAAAAATATTGAAAGGNGGGAAGCAAGGATATCCC
genomic: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCC
EST:
gi|33091506|gb|CF051500.1|CF051500EST: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCC
genomic: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCC
EST:
gi|6194533|gb|AW146637.1|AW146637EST: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATTCC
genomic: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCC
EST:
gi|33098069|gb|CF058029.1|CF058029EST: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTG ATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCC
genomic: AGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCC
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:
776AATGATATTAAAAGTATATCATCTGAAATGGAGGGTAAGACAGAAGAGGAAGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
276AATGATATTAAAAGTATATCATCTGAAATGGAGGGTAAGACAGAAGAGGAAGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
264AATGATATTAAAAGTATATCATCTGAAATGGAGGGTAAGACAGAAGAGGAAGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
318AATGATATTAAAAGTATATCATCTGAAATGGAGGGTAAGACAGAAGAGGAAGTTCAACGTTATGCTAGAGTTTTCAAGGAGAGATACAAGGAACTGAGTGgtaaggcagt ... gtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agatcaaactttccatactgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
tatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accattatattttttttttaataaaagcaactgtttgcatactgaagatcaaactttccatactgatggattgtgtatgttttgatcattgtacaaccagATTATGATAGAATTATAAAAAATATTGAAAGGGGGGAAGCAAGGATATCCCGCAAGGATGAGATTATGAAGGCTATTGGGAAGAAGCTAGACCGCTACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - -aataaaa
- - - - - - - - - - - - - gcaactg
- - - - - - - - - - - - - - - - - -tgcatac
- - - - - - - - - - - - - - - - - - - - - - - gatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtatg