Sequence
atgc intronic sequence ATGC exonic sequence...ttcccatttatctaatttccattgaactatacttttgttgtatgtttaaggaatatgtttttatggatagcattttaacacaagatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g67134.1 (Oryza sativa), 3'ss of exon 6
-------------------------------------------------------------ttcccatttatctaatttccattgaactata-cttttgttgta-tgtttaaggaatatgtttttatggatag--cattttaacacaagatgcttgt-tgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
| | || | | | ||| | | | || || ||| | | | ||| ||| ||| | | | | ||| | | |||||||||||||||||||||||||| || ||||||||||| || |||||||||||||| ||||||||||| || |||||||| ||| ||||||| ||||||||||
gtgtgttgtgctttgatcgcaactgttggctgctgtaataatagttgatttatcacttgaacatcaaattcctcagctcttttagaaacacaaccgttacgataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttttcttctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGT
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g67126.1 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------------------ttcccatttatctaatttccattgaactatacttttgttgta-tgtttaaggaatatgtttttatggatagc--attttaacacaagatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
|| ||| ||| | | ||| || | | || ||| | | | ||| |||| || | | | | ||| || |||||||||||||||||||||||||| || ||||||||||| || |||||||||||||| ||||||||||| || |||||||| ||| ||||||| ||||||||||
gtgtgttgtgctttgatctcaactgttggctgctgtaataatagttgatttgtcacttgaacatcaaattcatcagctcttttagaaacacaaccgtcaatataacctttggattgttgatctgtattagtagctcatgtggatatacttctcttctt-ctgcagGGAGCTTTGGATGGTGGTCTTGACATTCCTCACAGTGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGT
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G06590.1 (Glycine max), 3'ss of exon 6
ttcccatttatctaatttccattgaactatacttttgttgtatgtttaaggaatatgtttttatggatagc--attttaacacaagatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
|||| | || ||| || | || | ||| || | |||||| |||| | | || || | || ||||| | ||||||||| ||||||| || | |||||||||||||| || |||||||||||||| || | ||||| | ||| |||| ||||| || | || || || |
-----------gtaatct--atcatactgtaatgttaatcagtgt-----gattttgttttaatggttgatcaaattgaataatctgtgattgtt--tacagGGAGCTCTGGATGGGGGGTTGGATATTCCTCACAGTGACAAGAGGTTTGCTGGGTTTGATAAGGAGAAGAAGGAGCTTGATGCAGAGGTTCATCGGAAAT
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA16G03170.1 (Glycine max), 3'ss of exon 6
ttcccatttatctaatttccattgaactatacttttgttgtatgtttaaggaatatgtttttatggatagcattttaacacaagatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
|||| | || ||| | | | | ||| || | |||||| |||| | || || | | || | | | | ||||||||| ||||||| ||| | ||||||||||| || || |||||||||||||| || | ||||| | ||| |||| |||||||| | || ||||| |
-----------gtaatct--atcatactgcaatgctaattggtgt-----gattttgttttaatggtgatcaaattga-ataattttttattgtttacagGGAGCTCTGGATGGGGGTTTGGATATTCCTCATAGTGACAAGAGGTTTGCTGGGTTTGATAAGGAGAAGAAGGAGCTTGATGCTGAGGTGCATCGCAAAT
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA07G06580.1 (Glycine max), 3'ss of exon 6
ttcccatttatctaatttccattgaactatacttttgttgtatgtttaaggaatatgtttttatggatagc--attttaacacaagatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
|||| | || || || | || | ||| || | |||| |||| | | || || | || ||||| | ||||||||| ||||||| || | |||||||||||||| ||||||||||||||||| || | ||||| | ||| |||| |||||||| | || ||||| |
-----------gtaatct--atcatgctgtaatgttaatcagtgt------gattttttttaatggttgatcaaattgaataatctgtgattgtt--tacagGGAGCTCTGGATGGGGGGTTGGATATTCCTCACAGTGATAAGAGGTTTGCTGGGTTTGATAAGGAAAAGAAGGAGCTTGATGCTGAGGTTCATCGCAAAT
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA13G35580.2 (Glycine max), 3'ss of exon 6
ttcccatttatctaatttccattgaactatacttttgttgtatgtttaaggaatatgtttttatggatagcattttaacacaagatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
| | || || | || | | || | |||||| ||| || | | | || | ||| | ||||||||| ||||||| ||| | ||||||||||||||||| |||||||||||||| || | ||||| | ||| |||| |||||||| | || ||||| |
---------------------gtaatctctaatactgcaactcttggtatgattttgttttagtggtggtcaaatctaataattgtgatggtt--tacagGGAGCTCTGGATGGGGGTTTGGATATTCCTCACAGCGACAAGAGGTTTGCTGGGTTTGATAAGGAGAAGAAGGAGCTTGATGCTGAGGTTCATCGCAAAT
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT5G39740.2 (Arabidopsis thaliana), 3'ss of exon 6
----ttcccatttatctaatttccattgaactatacttttgtt--gtatgtttaaggaat-atgtttttatggatagcattttaacacaagat--gcttgtt-------gctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
| || || | || | || || || |||| || |||| | | | | | | | | ||||| || | | ||| | || ||||||||||||| || ||||| ||||| |||||||| || ||||| |||||||| ||| | || || | ||||| || |||||||| |||||| | || |
gtattgtgttttaatgtggttgtctgtgttcttatctgttgtatagtgtgttcatgatttgaagatgatgctagcaatcctttaataccctgttggtttgcttcatgaaactatagGGAGCTTTGGACGGAGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGTTTCCACAAAGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G25520.1 (Arabidopsis thaliana), 3'ss of exon 5
-----ttcccatttatctaatttccattgaactatactt--ttgttgtatgtttaaggaatatgtttttatggatagcattttaacacaa---------gatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
| ||| ||| ||| | | | ||| |||| | | | | | ||| || || | | ||||| | | || ||| ||| |||| ||||||||||||||||| ||||| |||||||| || ||||| |||||||| ||| | ||||| | ||||| || |||||||| |||||| | || |
gtattaacttgtttctctttttttgttgtgagtgctcttatttgtcattcttcttgagcaaatgcttatactggcaattctttaatatccttttggttcgctgtttgaatctgtagGGTGCTTTGGATGGTGGTCTTGATATCCCTCACAGTGACAAGAGATTTGCTGGGTTCCACAAGGAGAACAAGCAACTTGATGCTGAAATCCACAGGAACT
upper sequence: GRMZM2G090738_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 3'ss of exon 6
ttcccatttatctaatttccattgaa-ctatacttttg---ttgtatgtttaaggaatatgtttttatggatagcattttaacacaagatgcttgttg-ctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT----
| | ||| | ||| || || ||||| ||| || || || | || | | || || | | | | || | |||||||| ||||||||||| || |||||||||||||| || |||||||||||||| |||| | ||||| |||||| || ||||||||| | ||||||||||
---------aaatgattccagatgattctttaattttgaatttgcccattcaaaccatctcttcatcttgagcctcagcagttacctgtttcctcttaattccagggagCATTGGATGGTGGACTTGATATTCCTCACAGTGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATMapped 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|60395892|gb|DN228762.1|DN228762EST: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAG GGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
genomic: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
EST:
gi|60345048|gb|DN212021.1|DN212021EST: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAG GGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
genomic: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
EST:
gi|32846847|gb|CD986528.1|CD986528EST: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAG GGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
genomic: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
EST:
gi|166488230|gb|EG277394.1|EG277394EST: CTGGAAACCGTGTCTTTTGGTGCCCTCAAG GGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
genomic: CTGGAAACCGTGTC-TTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
EST:
gi|67024091|gb|CO452840.1|CO452840EST: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAG GGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
genomic: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
EST:
gi|60672209|gb|DN474977.1|DN474977EST: CGGCCTTATTAGGACTACTACTGGAAAACCGTGTCTTTGGTGCCCTCAAG GGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
genomic: CGGCCTTATTAGGACTACTACTGGAAA-CCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
EST:
gi|60347188|gb|DN214161.1|DN214161EST: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAG GGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
genomic: TCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCT
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:
385CTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
205CTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
182CTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
Block sizes:
49 (upstream exon),
48 (downstream exon)
Score:
88CTCTGTCGAGCCAGCGGAAGAGAGGAGGCCTTTCCGTGCCCTCTTAGATGTCGGCCTTATTAGGACTACTACTGGAAACCGTGTCTTTGGTGCCCTCAAGgtatattcct ... gttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaggaatatgtttttatggatagcattttaacacaagatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
ttttaac putative branch site (score: 88)
aatatgtttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcccatttatctaatttccattgaactatacttttgttgtatgtttaaggaatatgtttttatggatagcattttaacacaagatgcttgttgctgcagGGAGCTTTGGATGGTGGTCTAGATATTCCTCACAGCGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - -tttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgctt