Sequence
atgc intronic sequence ATGC exonic sequenceGGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatat-ttctttctgacatacctgctcttttttttgtttag
||||||||||||||||||||||||||| |||||||||||||||||||| || ||||||||||| || ||||||||||||||||||||||||||||| |||||||| | ||||| || || | ||| | ||| | | ||| || | | || || || ||||| ||| | |||||||| |||
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacaggagca---acctgttagaa-----ctaaaacatatttcagtacaagtcttttcttatctagattttttctaaca--------cccttttttgtatag
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatat-ttctttctgacatacctgctcttttttttgtttag
||||||||||||||||||||||||||| |||||||||||||||||||| || ||||||||||| || ||||||||||||||||||||||||||||| |||||||| | |||| | || || | ||| | ||| | | ||| || | | || || || ||||| ||| | ||||||||||| |||
GGCTAACAGTGCTAAAACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCCGAGGAGTTCCGGCTAGCACAAATATGTGGTCTCAATATTATTGTCCAGgtatatatacagga---ccaacctgttagaa-----ctaaaacatatttcagtacaagtcttttcttatctagattttttctaaca------cccttttttttgtatag
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA11G35460.1 (Glycine max), 5'ss of exon 23
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacat-acctgctcttttttttgtttag
||||||||||| |||||||||||||| || |||||||| ||||||||||| |||||||||||| | || || |||||||| || || |||||| |||||||| || | | | | | || ||| |||| | | ||| | | | || ||| | || | ||| | | || |
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCAGAGGAGTTCCGTTTGGCCCAGATATGTGGGCTTAACATTATTATTCAGgta-----atatgtttgtttgttgccaagtcttcaactaaattttgaaatgaactggaatttgt----ttttctttattcagctatcatctgatttacaattagaaagt
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA02G42560.1 (Glycine max), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgta-tacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctt--tctgacatacctgctcttttttttgtttag
||||||||| | || ||||||||||| || ||||||||||||||||| ||||||||||| ||| | || || || ||||| ||||| ||||||||||||||| || | | | ||||||| | | || | ||| | | | | | | | |||||| | | || || | | ||
AGCTAACAGTTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCGGAGGAGTTTCGTTTGGCCCAGATTTGTGGACTCAACATTATTGTTCAGgtaatatgttgatttcagtttttttgatgaactgtgt---gtgtgtgtgtatatatatatatataggaacgtctttcttaatttctgatgccagaccgagttc--------
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA18G02960.1 (Glycine max), 5'ss of exon 23
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgtttta--ttgcaaagtttctatgatatatttctttctgacatacctgctcttt--tttttgtttag------
||||||||||| |||||||||||||| || |||||||| |||||||||||||||||||| ||| | || || |||||||| || ||||||||| |||||||| | || || ||||| ||||||||||| | | || ||| || || | ||| | | | | | ||| | | ||| ||||
AGCTAACAGTGCAAAAACATGGAAGGAAGTTTGCTTTGCATGTGTTGACGCGGAGGAGTTTCGTTTGGCCCAGATATGTGGGCTTAATATTATTATTCAGgta-----------------atatgttgttttttgcctagtctttgactaaattttgaaatgaactggaatttgtttttcttt-attcagctgtcatctgatttccagttagaaagtt
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA02G39360.1 (Glycine max), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgta-tacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag
|| |||||| | |||||||||||||| || || |||||||||||||| || ||||| ||||| | || || || |||||||||||| | || ||||||| | | | ||| || || ||||||| | ||| | | | | | | | | | || || | || | | || ||
AGCAAACAGTTCAAAAACATGGAAGGAAGTTTGTTTTGCTTGTGTTGATGCTGAGGAATTCCGATTGGCTCAGATTTGTGGTCTCAATGTCATCATTCAGgtggcattctttttctagaatattttatcatttttc----atttttatcctg----ataatcccagttacccctgcctcactcaaattttcaatatagaaatttacta-
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: GLYMA14G06340.1 (Glycine max), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag
|| ||||| | || ||||||||||| || ||||||||||||||||| || |||||||| ||| | || ||||| ||||| || || |||||| |||||||| | | ||||||| | | | | | || | ||| | || || | ||| ||| |
AGCCAACAGCTCAAAGACATGGAAGGAAGTTTGCTTTGCTTGTGTTGATGCAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgttgatttcagttttttgatgaactgtgtgtgcccatgcacacgcgtgcgtgtatatataggaacgtttttctt--catttctgatgcagaccga------
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgattt--ttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag
|| |||||||| || ||||||||||| |||||||||||||||||||| || ||||| ||||| || || ||||| ||||| || || ||||| | ||||| | || || || | || || || || |||| | || || ||| | | | ||| | ||| | | || || |||| |
AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGTGTTGATGCTGAGGAATTCCGACTGGCTCAAATCTGTGGACTTAACATTATCATACAGgtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcctttttgtaatatttttgtgctttaatag------
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccct----agtctttgtttt--attgcaaagtttctatgat---atatttctttctgacatacctgctcttttttt--tgtttag---
|| |||||||| || ||||||||||| |||||||||||||| ||||| || ||||| ||||| | || |||||||||||||| || ||||| ||||||| | | | | | | | ||| |||| || || | ||| |||| | | ||| || | ||| | | | | | | | |||| || |||
AGCAAACAGTGCAAAGACATGGAAGGAAGTCTGCTTTGCTTGCGTTGATGCTGAGGAATTCCGGTTGGCTCAAATATGTGGTCTTAACATTATCATTCAGgtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctggttaatcttttggtgcttaatag
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtag-----gagggcatacttg-atgatttttccctagtctttgttt--tattgcaaagtttctatgatatatttctttctgac----atacctgctcttttttttgtttag------------------------------------
||||||||| | || |||||||||||||| ||||||||||||||||| || || |||||||| | || || |||||||||||||| |||||| | |||||| | | |||| | | | ||||| | || | | || | || |||| |||| | | ||| ||| | || | | ||||||| | | ||
GGCTAACAGCTCAAAGACATGGAAGGAGGTTTGCTTTGCTTGTGTTGATGCAGAAGAGTTCCGCTTAGCTCAGATATGTGGTCTCAACATTATTATACAGgtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttcc-ttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtag
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 5'ss of exon 12
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag
||| || || || ||||||||||| ||||||||||||||||| ||||| || |||||||| || || ||||| |||||||||||| ||||||| ||||||| | | | | || ||||| | | | | | | || | | | | ||| | || || || |||| || ||| | | | ||
GGCCAATAGCGCACGGACATGGAAGGAAGTCTGCTTTGCTTGTGTGGACGCCGAAGAGTTCCGCCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtat----ggataggtttctgctgttacattttgcaattagcctcatgattttactacgcaaccatgctt--ttcattactatcata--tgttctaatcgtactgaag
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 5'ss of exon 12
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaag---taggagggc----atacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacat-acctgctcttttttttgtttag
||| |||||||| || |||||||| ||||||||||||||||| || || || ||||| ||||| || ||||| |||||||||||| ||||||| ||||||| || | | || | | ||| | ||||| ||| || ||||| || | || || || | ||| | |||
GGCCAACAGTGCACGGACGTGGAAGGAAGTCTGCTTTGCTTGTGTGGATGCCGAAGAGTTTCGTCTGGCTCAAATTTGTGGTCTCAATGTTATTGTCCAGgtatgaaaagccttctaatgcttcgacatccgatcagttttcttgagttttctgtttatcaaggttctttccttgattagtttgttgtttcatgatgtgc----------------
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: EFJ13237 (Selaginella moellendorffii), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag
||| |||||||| || || ||||| || || ||||| ||||||||||||||||| |||||| | || |||||||||||||||||||| | ||||| |||||| ||| ||| || || || | | ||| |||||| || | | || | ||| | ||
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACGTCATTGTCCAGgta----------aggctatagtttctggttatactcta-tctttggttggt--ctaatctgttattaaatccag---------------------------------
upper sequence: GRMZM2G057576_T02 (Zea mays), 5'ss of exon 22
lower sequence: EFJ24508 (Selaginella moellendorffii), 5'ss of exon 24
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag
||| |||||||| || || ||||| || || ||||| ||||||||||||||||| |||||| | || |||||||||||||||||||| || ||||| |||||| ||| ||| || || || | | ||| |||||| || | | || | ||| | ||
GGCCAACAGTGCGAAGACGTGGAAAGAAGTTTGCTTCGCTTGTGTTGACGCGGAAGAGTTCAGGCTCGCACAAATATGTGGTCTCAACATCATTGTCCAGgta----------aggctatagtttctggttatactcta-tctttggttggt--ctaatctgttattaaatccag---------------------------------Mapped 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|67012270|gb|CO441019.1|CO441019EST: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG GTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
EST:
gi|32942182|gb|CF047001.1|CF047001EST: CTGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG GTTGATGACTTGGAAGAAGTCAGTGAGT
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGT
EST:
gi|32942004|gb|CF046823.1|CF046823EST: CTGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG GTTGATGACTTGGAAGAAGTCAGTGAGTA
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTA
EST:
gi|211133338|gb|FL220146.1|FL220146EST: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG GTTGACGACCTGGAANAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
EST:
gi|67024143|gb|CO452892.1|CO452892EST: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG GTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTC
EST:
gi|32942430|gb|CF047249.1|CF047249EST: CTGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAG GTTGATGACTTGGAAGAAGTCAGTGAGTA
genomic: CGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTA
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:
383GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
281GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
257GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
482GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagt ... ttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCTAACAGTGCTAAAACATGGAAGGAGGTCTGCTTTGCTTGTGTTGACGCGGAGGAGTTCCGTCTTGCACAAATATGTGGTCTCAATATTATTGTTCAGgtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttag
- - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG