Sequence
atgc intronic sequence ATGC exonic sequencegtgagcttgttctttgctcttattgatagcttctttttcgcctgagctaatgcatcttccctaattgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G150772_T02 (Zea mays), 3'ss of exon 20
lower sequence: LOC_Os09g24260.1 (Oryza sativa), 3'ss of exon 20
gtgagcttgttctttgctcttattgatagctt----ctttttcgcctgagctaatgcatcttccctaattgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
|| ||||| ||| ||||| || | || || || ||| || ||| ||||| | | | || ||||||| |||||||||| |||||||| ||||||||||| ||||||||||||||||| || || || |||||||||||||||||||| ||||||||||||||||||||||
gtaagcttaatctgtgctcataatcatccttttgttctcttttgcttgatctaatactttcttccatattgttt-agATCATGCGGTGCAATTACGCAATCAAAGCCCTCCGGTTCTCTACTGCTCTTTCGATCTTGAAAGATGAGTTCCTGCGTTCCAGAGATTATCCTCAATGCC
upper sequence: GRMZM2G150772_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA17G20310.1 (Glycine max), 3'ss of exon 21
gtgagctt-----gttctttgctcttattgata-gcttctttttcgcctgagctaatg--catcttccctaattg-ttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
|| ||| | ||| ||| |||| | || | || |||| || || ||| | ||| | |||| | ||||| | |||||| | |||||||| || || || ||||| | |||||||||||||| || ||||| |||||||||||||| |||| |
gtaagcatcataaattccttgttcttggcattttagttttggtttttctgaacttctgaccatgtgaatattttgatcttagGTGATGCGAGGTGTTTATGCTGTGAAAGCTCTTCGTTTTTCCACTGCTTTAAATATTTTGAAAGATGAATTTCTGCGTTCCAGAGATTATCCAAAATGTC
upper sequence: GRMZM2G150772_T02 (Zea mays), 3'ss of exon 20
lower sequence: GLYMA05G10590.1 (Glycine max), 3'ss of exon 21
gtgagcttgttctttgctct--tattgatagcttctttttcgc----ctgagctaatgcatcttccctaatt---gttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
|| ||| | ||| | | |||| | || |||| | |||| || || || ||| | |||| | ||||| | |||||| | |||||||| | || || ||||| | |||||||||||||| || ||||| |||||||||||||| |||| |
gtaagcaacataaatgccttgttcttgacattttagttttggtttttctgaacttctgagcatttgaatattttgatcttagGTGATGCGAGGTGTTTATGCTGTGAAAGCTCTTCATTTTTCCACTGCTTTAAATATTTTGAAAGATGAATTTCTGCGTTCCAGAGATTATCCAAAATGTC
upper sequence: GRMZM2G150772_T02 (Zea mays), 3'ss of exon 20
lower sequence: Vv00s1501g00010.t01 (Vitis vinifera), 3'ss of exon 4
--------------gtgagctt-gttctttgctcttattgatagcttctttttcgcctgagctaatgcatcttccct-aattgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
||| | | ||| ||| | | || || || ||||| | || | || || | | ||| | || | |||| | | || ||||||||||||||||| || |||||||| |||| ||||||| ||||| ||||| || || || |||||||| ||||| |
gtgggctatggtttgtgtgttaagtttttttccatgttttatgaattttttttt---ttagtttctgaatttgttgtgaataaaatcagGTATTGCGGGGTAGCTACGCAATCAAAGCTCTCCGTTTTTCTACTGCTTTGTCTGTTTTGAAGGATGAATTCCTACGATCTAGGGATTATCCACAATGTC
upper sequence: GRMZM2G150772_T02 (Zea mays), 3'ss of exon 20
lower sequence: Vv00s0379g00010.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtgagctt-gttctttgctcttattgatagcttctttttcgcctgagctaatgcatcttccct-aattgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
||| | | ||| ||| | | || || || ||||| | || | || || | | ||| | || | |||| | | |||||||||||||||||||| || ||| |||| |||| ||||||| ||||| ||||| || || || |||||||| ||||| |
gtgggctatggtttgtgtgttaagtttttttccatgttttatgaattttttttt---ttagtttctgaatttgttgtgaataaaatcagGTATTGCGGGGTAGCTATGCAATCAAAGCTCTCCGTTTTTCTTCTGCTTTGTCTGTTTTGAAGGATGAATTCCTACGTTCTAGGGATTATCCACAATGTCMapped 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|13315888|gb|BG410236.1|BG410236EST: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAA ATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
genomic: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
EST:
gi|149014442|gb|EE044051.2|EE044051EST: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAA ATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
genomic: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
EST:
gi|32837707|gb|CD977385.1|CD977385EST: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAA ATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
genomic: GTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
EST:
gi|32838041|gb|CD977719.1|CD977719EST: TGGAGACC-TGNCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAA ATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
genomic: TGGAGACCTTG-CTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTG
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:
355ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
293ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
278ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
385ACGGATCACTCCAAGGTCATTGGACATATTAACTAAAGGACCTCCTGTTTGTGGAGACCTTGCTGTATCATTATCTCAAGCAGGACCTCAGTTTACCCAAgtgagcttgt ... attgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttattgatagcttctttttcgcctgagctaatgcatcttccctaattgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
ccctaat putative branch site (score: 385)
ttgtttt CT-rich tract
taattgtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcttgttctttgctcttattgatagcttctttttcgcctgagctaatgcatcttccctaattgttttagATCATGCGCTGCAATTATGCAATCAAAGCTCTCCGGTTCTCTACTGCGCTGTCAATTTTGAAAGATGAGTTCCTGCGCTCCAGAGATTATCCTCAATGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG