Sequence
atgc intronic sequence ATGC exonic sequence...ctttttcttgggatacagcatttgttatgctgaacgttttcagaacttgttctgaatctataatgttccattatccggttgctaaccaaggttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g40030.2 (Oryza sativa), 3'ss of exon 4
ctttttcttgggatacagcatttgttatgctgaacgttttcagaactt------gttctgaatctataatgttccattatccggttgcta--accaaggttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
|| || ||| ||| ||| || ||| |||||| | ||||||||| | || || | | || | || | |||| || ||| |||| ||||||||||||||||| ||||||||| | ||||||||||||||| |||| ||||||||||||||||||||||||||||||||||||||||||||||||
--------tgtagcacttgttttcttacgctaaaaatttccagaacattgttatgttctgaatatgccatattttactttctgattttttttaccatgggtttgtcagCGTGGCTTTGATTGTATTTGGAGCATTTATCGCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G25900.1 (Glycine max), 3'ss of exon 3
--ctttttcttgggatacagcatttgttatgctgaacgttttcagaacttgttctgaatctataatgttccattatccggttgctaaccaaggttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACAT-TACAACA
| || | || ||||||| | | | | ||| | | | || ||||| | || | | | || | || |||||||| | | || || ||| || ||||||||||||||||| |||||| ||||||||||| | ||| | |||| ||||| | ||||| | ||
tgatcaacgttagttgttagtttttgttactttttgagctagatatgttagttttagagcgattatgtttctttgcctaacgg--actaaatgattcatcagTGTTGGGATAATCATAGCCGGTGCTTTTGTTGCTGGAGCTCGTGACTTGGCATTTGATGCTTTTTCCTATTCAGTTGTATTTGTAGAAAACATGTGTAAG-
upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA06G07120.1 (Glycine max), 3'ss of exon 2
ctttttcttgggatacagcatttgttatgctgaacgttttcagaacttgttctgaatctataatgttccattatccggttgctaaccaaggttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
||| | | | | | | | || | ||| || | | | | | |||| | | | | | | |||||||||| | |||||||| ||||| ||||||||||| ||||| || || || || |||||||| | ||| ||||| ||||| || || | ||||| || |||
ttttccactataactgaatgaagttaaagttcaaattgttctttgaatgaacatctccctgattccttcatttaactgaaatttgtaaggttgttatcagTGTTGGCTTGATTGTCTTCGGTGCATTTGTTGCGGGAGCACGGGATTTATCCTTTGATGCCCATGGCTATGCCATTGTTTTCCTGTCAAACATCACCACA
upper sequence: GRMZM2G020976_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv11s0016g05710.t01 (Vitis vinifera), 3'ss of exon 4
ctttttcttgggatacagcatttgttatgctgaacgttttcagaacttgttctgaatctataatgttcc--attatccggttgctaa---ccaaggtttt-atcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
|| | | ||| | | | | || | | | | | ||| ||||| | ||| || || || |||| |||| | |||||| | | || || | || |||||| ||||||||||||| ||| |||||||||| | ||| ||||||||||| |||||||| |||||| |||
------ctcagactgatttattcttggaattttatagtgatagcatcattacctattgtatcatgttgctaattttctcaatggaaatttccaaaattttcaccagTGTTGGGATAATCATACTTGGTGCATTTATTGCTGGAGCTCGGGACCTGTCATTTGACTCCTATGGCTATGCTATTGTTTTTGTGGCAAACATTTGTACAMapped 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|71298002|gb|DR784970.1|DR784970EST: ATGGAGTATTTCCTGGCAAAGCAGAAGCAC-CCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTG
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTG
EST:
gi|74233566|gb|DT641480.1|DT641480EST: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
EST:
gi|31353270|gb|CD437627.1|CD437627EST: ATGGAGTATTTCCTGGCAAAGCAGAGGCACACCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
EST:
gi|71767957|gb|DR965894.1|DR965894EST: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
EST:
gi|71420101|gb|DR805011.1|DR805011EST: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
EST:
gi|78076866|gb|DV505300.1|DV505300EST: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
EST:
gi|71420100|gb|DR805010.1|DR805010EST: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
EST:
gi|31355902|gb|CD440259.1|CD440259EST: ATGGAGTATTTCCTGGCAAAGCAGAGGCACACCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
EST:
gi|148947455|gb|EC892886.2|EC892886EST: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAG TGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
genomic: ATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTC
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:
48 (upstream exon),
48 (downstream exon)
Score:
49TTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
Block sizes:
45 (upstream exon),
49 (downstream exon)
Score:
89TTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
Block sizes:
48 (upstream exon),
49 (downstream exon)
Score:
151TTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
Block sizes:
43 (upstream exon),
49 (downstream exon)
Score:
37TTCCTATGTATACAACTCTACGACGCACAACAGTCGTGTTTACAATGACAATGGAGTATTTCCTGGCAAAGCAGAAGCACACCCCACCTATAATAGGCAGgtaaatatat ... gttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgttctgaatctataatgttccattatccggttgctaaccaaggttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
tgctaac putative branch site (score: 37)
ttttatc putative PPT
aatctataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttttcttgggatacagcatttgttatgctgaacgttttcagaacttgttctgaatctataatgttccattatccggttgctaaccaaggttttatcagTGTGGCTTTGATTGTATTCGGAGCATTTGTTGCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACA
- -tttcttg
- - - - - - -tacagca
- - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggttgct