Sequence
atgc intronic sequence ATGC exonic sequencegtagtcattttcttttgttatattaggactcgaacccgttaatccagctcagtctctatgttgatcttcagagttttggaaattgttttactgtatagagcttactgttctctctaacaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os03g22420.1 (Oryza sativa), 3'ss of exon 20
gtagtcattttcttttgttatattaggactcgaacccgttaatccagctca-gtctctatgttgatcttcagagttttggaaattgttttactgtatagagcttactgttct--ctctaacaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
|| | | | || || | || | || | | || || | || || | || || ||||||| ||| || ||||||| ||||||||||||||| || ||||| ||||||||| | |||||||| |||||||| || || | ||||| ||||| ||||||||||||||||| || || ||||
----------------------------cttcaccttctctggtcaatgcatgcctgaacgtgtagtgttgcagcattatatctt-ttaaaatgcatggagcttatgaatcttgctataacaatttcagGATATTGCTACTGAGAATGAATTTGAAAAGCGACTTCTTGCTGATGTTATACCCCCGGACGAAATAGGTGTCACCTTTGAGGACATTGGGGCATTGGAAA
upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA04G37050.1 (Glycine max), 3'ss of exon 3
-----------------gtagtcattttcttttgttatattaggactcgaacccgttaat--ccagctcagtctct--atgttgatcttc----agagttttggaaattgttttactgtatagagcttactgt----tctctctaacaat-------gtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
| | ||| || || | || ||| | ||| | ||| || | | | | ||| ||| ||||||| ||| ||| || || | | ||| || |||| | | ||||||| ||| || ||||| |||||||||||||||||| | || |||||||| || || |||| || |||||||| ||||| || ||||||||| | ||||
gtgattgttatggacttttgctgctttgattgtgagagatagtgacatccagtagtttgttcccaacttactgcttggaagttattctgttgatagagtttaatcgatttatttcatgaatgttgtgttctgaattatccctcttatgttttttgaaatcagGATGTTGTAACAGAAAACGAGTTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAATGACATTGGTGTTACTTTTGATGATATTGGAGCTCTTGAAA
upper sequence: GRMZM2G042074_T01 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA05G03270.1 (Glycine max), 3'ss of exon 16
gtagtcattttcttttgttatattaggactcgaacccgttaatccagctcagtctctatgttgatcttcagagttttggaaattgttttactgtatagagcttactgttctctctaacaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
|| ||| | || || | || ||| || || | ||||||| | ||| | | || | | || | || | || | || | | ||||||| ||| || |||||||| ||||||||||||||| | || |||||||| || || ||| |||| |||||| ||||| || ||||||||| | ||||
---gtgattgt-ttgtgcccttttgctactt--acatgtgattccagctttgct--tattacaagttattctgtcgggagagttcataaacactgtattctaaatcattttgcttgc-----tcagGATGTTGTGACAGAAAATGAATTTGAAAAGAGGCTTTTGGCTGATGTTATTCCACCTAGTGACATCGATGTTACTTTTGATGATATTGGAGCTCTTGAAAMapped 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|67017525|gb|CO446274.1|CO446274EST: AAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAG GATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATC
genomic: AAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAGgtagtcattt ... acaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATC
EST:
gi|67033220|gb|CO461969.1|CO461969EST: NAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGGAATCACTGAAG GATATTGCTACGGAAAATGAGTTNNGAANAGAG-CTTCNTGCAGATGNTAT
genomic: AAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAGgtagtcattt ... acaatgtcagGATATTGCTACGGAAAATGAGTTT-GAAAAGAGGCTTCTTGCAGATGTTAT
EST:
gi|31359802|gb|CD444159.1|CD444159EST: AAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAG GATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATC
genomic: AAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAGgtagtcattt ... acaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATC
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),
48 (downstream exon)
Score:
225CCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAGgtagtcattt ... acaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
273CCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAGgtagtcattt ... acaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
239CCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAGgtagtcattt ... acaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
339CCTTAAGCATGGTATTGACATGTTGGAAAGTATCCAGTCTGGCTCGAAGAGCAGCACTAAAAGGAAATCACTGAAGgtagtcattt ... acaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agttttggaaattgttttactgtatagagcttactgttctctctaacaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
ctctaac putative branch site (score: 339)
aaattgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtcattttcttttgttatattaggactcgaacccgttaatccagctcagtctctatgttgatcttcagagttttggaaattgttttactgtatagagcttactgttctctctaacaatgtcagGATATTGCTACGGAAAATGAGTTTGAAAAGAGGCTTCTTGCAGATGTTATCCCTCCACATGAAATCGGTGTTACCTTTGAGGACATTGGAGCTTTAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT