Sequence
atgc intronic sequence ATGC exonic sequencegtcagtatttggactccatgcaacaacaaaataataataataataataaacagattcgttatattggaaggtgcctccaaatagcactcctcattaccttgtatatgtttatctgtttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os02g04710.1 (Oryza sativa), 3'ss of exon 14
gtcagtatttggactccatgcaacaacaaaataataataataataataaacagattcgttatattggaaggtgcctcca---aatagcactcctcattaccttgtatatgtttatctgtttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
|| |||| ||||| || | | | ||||| || | | | | | ||| || |||| |||| || | | | ||| |||| | | | | | ||||| |||||||||| ||||||||||||||||| || || ||||| ||||||||||| |||||| || ||||||||||||| ||||| | | ||||||||||||||||
gttagtacaaggacttcac---atgaaacaataagaacattgcgtgcatata-attgtctacattgtctactgcccttggtcaaaaaaaaaattgtctacattgttcac-tctgtat-tttccaacagGTATGGTTCTTGGGCTGTTTGTTTTACCTATGGCACATGGTTTGGTGTAAAGGGATTAGTTGCTGCTGGTAGGACATTCAAAAACAGTCCTGCAATCAGA
upper sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 14
lower sequence: GLYMA01G00430.1 (Glycine max), 3'ss of exon 15
gtcagtatttggactccatgcaacaacaaaataataataataataataaacagattcgttatattggaaggtgcctccaaatagcactcctcatta--ccttgtatatgtttatctgtttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
|| || | | | | ||| ||| ||| | | | | | || | | || ||| || ||| || || | ||| | |||||||||| ||||||| ||||| ||||| ||||| |||||||||| || || || || ||||||||||| || | || | | | ||| |
----------------------actctttgttatttttctttctttctgccagcttc--tatttctgcatgaaattg-aactttctctgttcagtagacctctaatcacttaaactgct--aaacagGTATGGTTCTTGGGGAGTTTGCTTCACTTACGGTGCTTGGTTTGGGGTAAAAGGTCTGATTGCTGCTGGAAGGAGTTTCAGTAATTGCTCAAGCATCCGT
upper sequence: GRMZM2G065494_T01 (Zea mays), 3'ss of exon 14
lower sequence: AT2G07050.1 (Arabidopsis thaliana), 3'ss of exon 14
gtcagtatttggactccatgcaacaacaaaataataataataataataaacagattcgttatattggaaggtgcctccaaatagcactcctcattaccttgtatatgtttatctgt----ttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
| | ||| || || | || || | | ||| | | | || |||||| | || || || || || || | | || | | |||| || | |||||||| || ||||||||||| |||||||| || || |||||||| ||||| || || | |||| ||| | |||||| | | | ||| |
-------gtaagtctctattcattataaatctatttgcag-aattacatat---tttcctatattt-----tatctttgtat----cttctagttggtttctttttggtaacctgtgatatttccctagGTATGGATCATGGGCTGTTTGCTTCACGTATGGTACGTGGTTTGGAGTGAAAGGGCTGGTAGCTGTTGGAAAAACATTGAAAAACTCTCCACATGTTGCTMapped 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|60400796|gb|DN233603.1|DN233603EST: AAGTGACGGTTCATG GTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAA
genomic: AAGTGACGGTTCATGgtcagtattt ... tttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAA
EST:
gi|17352566|gb|BM173680.1|BM173680EST: AGCAAAGCTGCTAATTTCATTGAGAGCATTCAGAAAAGTGACGGTTCATG GTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAA
genomic: AGCAAAGCTGCTAATTTCATTGAGAGCATTCAGAAAAGTGACGGTTCATGgtcagtattt ... tttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAA
EST:
gi|31357306|gb|CD441663.1|CD441663EST: AGCAAAGCTGCTAATTTCATTGAGAGCATTCAGAAAAGTGACGGTTCATG GTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAA
genomic: AGCAAAGCTGCTAATTTCATTGAGAGCATTCAGAAAAGTGACGGTTCATGgtcagtattt ... tttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAA
EST:
gi|31357419|gb|CD441776.1|CD441776EST: ATTGAGAGCATTCAGAAAAGTGACGGTTCATG GTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAA
genomic: ATTGAGAGCATTCAGAAAAGTGACGGTTCATGgtcagtattt ... tttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAA
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),
49 (downstream exon)
Score:
154TCAGAAAACTATACCCTGGGCACCGCAGGAAAGAGGTGGACAGCTGTATCAGCAAAGCTGCTAATTTCATTGAGAGCATTCAGAAAAGTGACGGTTCATGgtcagtattt ... tttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
187TCAGAAAACTATACCCTGGGCACCGCAGGAAAGAGGTGGACAGCTGTATCAGCAAAGCTGCTAATTTCATTGAGAGCATTCAGAAAAGTGACGGTTCATGgtcagtattt ... tttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
130TCAGAAAACTATACCCTGGGCACCGCAGGAAAGAGGTGGACAGCTGTATCAGCAAAGCTGCTAATTTCATTGAGAGCATTCAGAAAAGTGACGGTTCATGgtcagtattt ... tttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
Block sizes:
48 (upstream exon),
48 (downstream exon)
Score:
197TCAGAAAACTATACCCTGGGCACCGCAGGAAAGAGGTGGACAGCTGTATCAGCAAAGCTGCTAATTTCATTGAGAGCATTCAGAAAAGTGACGGTTCATGgtcagtattt ... tttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcctccaaatagcactcctcattaccttgtatatgtttatctgtttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
tctgtttcc CT-rich tract
ttgtatatgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagtatttggactccatgcaacaacaaaataataataataataataaacagattcgttatattggaaggtgcctccaaatagcactcctcattaccttgtatatgtttatctgtttccgacagGTATGGCTCTTGGGCTGTTTGTTTCACGTACGGCACTTGGTTTGGTGTGAAGGGACTAATTGCTGCTGGTAGAACATTTGAGAGCAGTCCTGCAATCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG