Sequence
atgc intronic sequence ATGC exonic sequencegcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacatgatgctttgctttttattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 30
----------------gcaag-tgatttcttcagaatgcttaaatgcataccttctcttgttcact-ttgttcatac-atgatgctttgctttttattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
|| | | | | ||| | ||| ||||| || || || || ||||||| | |||||| | ||| | ||| | ||| |||||||||| ||||| |||||||||||||||||||||||||| || ||||| |||||| | ||| ||||||| ||| ||||||||
gcaagttataattttaacatgctaggaagctaggcatgtccatatgtgtacctccttttcttgaccgctgttcatgccatgatgtat--cttctgattctgcagAGGAGAGATGTTTATGGAGCTTGGGAACAATACCTTGGCTTGGAACATACTGACACAACACCAAAAAGGTCTTATACAGCCAATCAG
upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA20G11330.1 (Glycine max), 3'ss of exon 22
--------------gcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacatgatgctttgctttttattatac---agCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
| || | ||| | | || | | || | | | || | ||||| ||||| | ||| || ||| || || | |||||||| |||||||||||||| ||||| ||||| |||||||| ||||| | | | ||| | || || | ||| |||
gttgagacttcattgtaattttttttcttaaaaagat---atccgctatattcatgtttgaatttgtgattacattgtacttgttttggtatcctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGTTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG
upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 30
--------------------gcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacatgatgctt-tgctttttattat-acagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
| ||| || || || ||| ||| | | || | || | | |||||| | | | || | | || |||||||||| |||||||||||||| ||||| ||||| |||||||| ||||||| | | ||| | || || | || |||
gtacattcatttatacttggattccttttttttttgtgataattcaattgatatttagcatcatttttatatgtctgaatttatgcttgcattgtatcttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGTTTGGAGCATACTGATAATGCTCCTAAAAGATCATATGCTGTTAACCAG
upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA13G16040.1 (Glycine max), 3'ss of exon 11
--------------gcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacatgatgctttgctttttattatac---agCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
| || | ||| | | || | | || || | | || ||||| ||||| ||| || ||| || || | |||||||| |||||||||||||| ||||| |||||||||||||| ||||| | | | ||| | || || | ||| |||
gttgagacttcattgtaattttttttcttaaaaagtt---atccactgtattcatgtttttatttgtgattacattgcacttgttttggtatcctatgatagAGAAGAGATGTTTATGGTGCTTGGGAGCAATATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTCAACCAG
upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 30
-------------------------gcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacatgatgctt-tgctttttattat-acagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
| || || || || ||| ||| | || | | || | | |||||| | | | || | | || |||||||||| |||||||||||||| || || |||||||||||||| ||||| | | | ||| | || || | || |||
gtacattcatttatacttggattccttttttttttggtttgtgataattcaattgatatttagcaccattttcatatgtctgaatttatgcttgcattgtatcttgtgatagAGGAGAGATGTTTATGGTGCTTGGGAGCAGTATCTTGGCTTGGAGCATACTGACAATGCTCCTAAAAGATCATATGCTGTTAACCAG
upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 30
------------------------------------gcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacat--gatgctttgctttttattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
|| || | | || || | | | | | || | | || | | ||| |||| ||| | || | ||| | |||||||| ||||||||||||||||| |||||||| |||||||| ||||||| | | ||| || |||| || | ||||||
gtgtcttaaatttaaaattatttttttcttgtgaatgccgatggcctgtgcaaaacttgtgatttatcctgatagggtttttattgaatttcgagtttaaatgttttggtttattttgttcagAGAAGAGATGTTTATGGTGCTTGGGAACAGTACCTTGGGCTGGAGCACTCTGATACTGCTCCTAAAAGGGCTTATGCAGCAAATCAG
upper sequence: GRMZM2G303655_T01 (Zea mays), 3'ss of exon 19
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 30
gcaagtgatttcttcagaatgcttaaatgcatac-cttctcttgttcactttgttcatacatgatgctttgctttttattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
| | || || | | | || | || | | | | | ||| || ||| ||||| | | ||| | |||||||| |||||||||||||| || || ||||| ||||||||| | || | | | ||| |||| || || | ||||||
gtctctctttctctctctctctctctctcaatgtgccacttgtttggattccacttttacccaat-ttttattttttgcttttcagAGAAGAGATGTCTATGGTGCTTGGGAGCAGTATCTTGGTTTGGAGCACTCCGACAATGCTCCCAAAAGGTCATATGCAGCTAATCAGMapped 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|60357459|gb|DN224432.1|DN224432EST: ACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG CGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
genomic: ACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
EST:
gi|71767531|gb|DR965468.1|DR965468EST: ACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG CGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
genomic: ACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
EST:
gi|67032245|gb|CO460994.1|CO460994EST: CCGGCCAGAGTACCCTCCAG-ACACTGACGTTGTATCAGCACGTTTTCAG CGGAGAGATGTATATGGTGCTTGGGAAACA-TACCTTGGCTTGGAGCACAC
genomic: CCGGCCAGAGTACC-TCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAA-CAATACCTTGGCTTGGAGCACAC
EST:
gi|47962024|gb|CN844733.1|CN844733EST: ACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG CGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
genomic: ACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
EST:
gi|60396957|gb|DN229776.1|DN229776EST: GTTGTATCAGCACGTTTTCAG CGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
genomic: GTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
EST:
gi|60346259|gb|DN213232.1|DN213232EST: ACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAG CGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
genomic: ACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACT
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:
578TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
414TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
361TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
469TGGAAGCTTGCATTCATATCCATGAACCGGCCAGAGTACCTCCAGGACACTGACGTTGTATCAGCACGTTTTCAGgcaagtgatt ... tattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataccttctcttgttcactttgttcatacatgatgctttgctttttattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
ctttgctttttatt CT-rich tract
tttgctttttattata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaagtgatttcttcagaatgcttaaatgcataccttctcttgttcactttgttcatacatgatgctttgctttttattatacagCGGAGAGATGTATATGGTGCTTGGGAACAATACCTTGGCTTGGAGCACACTGATACAACATCGAAACGGTCTTACACATCCAATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA