Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttttttgcttttcgtatgtgttctgaactgaataggttatctgaattttctgtgcagtattgctcattgttgaaaatttcttttagactagagagagttattgtatgtgttatattttctccaaaattaaggattgtatggtcatcgacctttttgatagccattacttactgatgttatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 3'ss of exon 6
gtgagtttttttgcttttcgtatgtgttctgaactgaataggttatctgaattttctgtgcagtattgctcattgttgaaaatttcttttagactagagagagttattgtatgtgttatattttctccaaaattaaggattgtatggtcatcgacctttttgatagccattacttactgatgt-tatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
| || | || ||| ||| | | | || || | || |||| ||| | | | || ||| | || | ||||||| | | | | |||||||||| |||||||| | |||||| || || ||||||||||||||||| ||||||||||| ||| | ||||| ||
---------------------------------------------------------------------------------------tctaatgttgat---gttgaaaggtgtctcaaagttgggtcactgt-aatgatt--atgattag-gttctgttttacagt-agtacttaccattctatttatttgcagGCTAATGGTTCTTAGAATCAGTTCAAAATTTGAACTGAGAAGATTTTGCCGTACTACAGGGTCCATTGCACTT
upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G26920.1 (Glycine max), 3'ss of exon 6
gtgagtttttttgcttttcgtatgtgttctgaactgaataggttatctgaattttctgtgcagtattgctcattgttgaaaatttcttttagactagagagagttattgtatgtgttatattttctccaaaattaaggattgtatggtcatcgacctttttgatagccattacttactgatgttatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
| |||| || || | | | | ||| | | | | || || || || || | | || | || ||| | ||| | | | || ||||||||| |||||||||||||||||||| ||||||||||| | |||| ||||| || ||||| ||||||| ||
-----------------------------------------------------------------------gtatgtgaagtctttattcatgtttggtggttttaat-tgtctcttgctattaaattaatatgaacattataacttacaagtgcacattagattg---ttaacttcaaaatccctgcttgcagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACTGGTTCTGTTGCCATG
upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 6
gtgagtttttttgcttttcgtatgtgttctgaactgaataggttatctgaattttctgtgcagtattgctcattgttgaaaatttcttttagactagagagagttattgtatgtgttatattttctccaaaattaaggattgtatggtcatcgacctttttgatagccattacttactgatgttatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
| |||| || | | | | | ||| | ||| | || | | |||||| || | | | | || | || | | | | || || ||||| |||||||||||||||||||| ||||||||||| | |||| ||||| || || || ||||||| ||
-----------------------------------------------------------------------gtatgtgaagtctttatccatgtttggtggttttaat---tgtctcttactatt----gaattaatatgaacattataactgcacattagattgttttctaacttcaaaattcctgcttttagGCTTATGGTTCTGAAAATCAGCTCAAAGTTTGAACTACGTCGATTTTGCCGGACAACCGGCTCTGTTGCCATG
upper sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 6
gtgagtttttttgcttttcgtatgtgttctgaactgaataggttatctgaattttctgtgcagtattgctcattgttgaaaatttcttttagactagagagagttattgtatgtgttatattttctccaaaattaaggattgtatggtcatcgacctttttgatagccattacttactgatgttatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
||| | ||| || | | || || ||| | | | | | | | || | |||||| ||| | || | || | | | || |||||| || |||||| ||||||||||||| |||||||||||| | |||| |||||||| ||||| ||||||||| ||
---------------------------------------------------------------------------ttgcatcttttcttcat-caagggatgcatatc-caagaagaacaatctatgcatg--------tggtatgg----cgatgt-----atgaactgaaccagtttgtttcttgcttgcagACTTATGGTTTTGAAAATCAGCTCAAAGTTTGAACTGCGGCGATTTTGCCGTACAACTGGAGCTGTTGCAGTTMapped 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|211512561|gb|FL110022.1|FL110022EST: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAA GCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAA
genomic: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAA
EST:
gi|6626281|gb|AW257813.1|AW257813EST: AGTGGAGCTGCAGTTGGTGACATGGCACTACATTTTTGTGAACGTTACAA GCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCG
genomic: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCG
EST:
gi|60396537|gb|DN229406.1|DN229406EST: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAA GCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCG
genomic: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCG
EST:
gi|24773918|gb|CA409172.1|CA409172EST: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAA GCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCG
genomic: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCG
EST:
gi|60358557|gb|DN225530.1|DN225530EST: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAA GCTGATGGTTCTGAAAATCATCTCGAAGTTTGAACTGAGAAGATTCTGCCC
genomic: AGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCG
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:
368TGGAGGAGCTTATAAAAGCTGTTGCTGACTCAGGTGCCAAGGTTATTGTCAGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
198TGGAGGAGCTTATAAAAGCTGTTGCTGACTCAGGTGCCAAGGTTATTGTCAGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
127TGGAGGAGCTTATAAAAGCTGTTGCTGACTCAGGTGCCAAGGTTATTGTCAGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
149TGGAGGAGCTTATAAAAGCTGTTGCTGACTCAGGTGCCAAGGTTATTGTCAGTGGAGCTGCAGTTGGTGACATGGCGCTACATTTTTGTGAACGTTACAAgtgagttttt ... atgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtatggtcatcgacctttttgatagccattacttactgatgttatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
tttttgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttttttgcttttcgtatgtgttctgaactgaataggttatctgaattttctgtgcagtattgctcattgttgaaaatttcttttagactagagagagttattgtatgtgttatattttctccaaaattaaggattgtatggtcatcgacctttttgatagccattacttactgatgttatgtttgcagGCTGATGGTTCTGAAAATCAGCTCGAAGTTTGAACTGAGAAGATTCTGCCGTACTACTGGGGCTGTTGCAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT