Sequence
atgc intronic sequence ATGC exonic sequence...cttgttgtcattgattgatgtccttgagtctgtgaaggaaaacagctagtgctctgaaattttagctcgttggcatgaatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g03260.3 (Oryza sativa), 3'ss of exon 12
cttgttgtcattgattgatgtccttgagtctgtgaaggaaaacagctagtgctctgaa-attttagctcgttggcatgaatctggtaacctggatg--tgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
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-tccttaatgcaaagggaattgcaagtgttctccaaattatatc-ctgttgatgcgagtggttttgttgattaac-tgatttcaaaaacgtatttgggtgcagGTGTGTGTGTCGACGACGAACAGGAATTTCCCCGGCAGGATGGGGCACAAGGAAGGGCAGATCTACCTGGCTTCGCCGTTCACCGCGGCGGCTTCAGCCC
upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 14
--cttgt-tgtcattgattgatgtccttgagt-ctgtgaaggaaaacagctagtgctctgaaattttagctcgttggcatgaat-ctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
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tgttcatctgccat--atggttgcttttatatgctttctacataaatgatgaga---ttgagagtctgagtaatttactccattgcctacgtgctggttgtgcagGTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAGGAAGGTCAAATCTATTTGGCTTCCCCTTATACAGCTGCTGCATCTGCAT
upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 14
cttgtt-gtcattgattgatgtccttgagtctgtgaaggaaaacagctagtgctctgaaattttagctcgttggcatgaatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
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-ttgttcatctgccatatggttgcttttgtatgctttctacataagtgatgagattgagaatctgagtatttactccattgtttacacgctggttgtgcagGTTTGTGTTTCAACTACGAACAGGAACTTCCCGGGCCGAATGGGACACAAGGAAGGTCAAATCTATTTGGCTTCCCCATATACAGCTGCTGCATCTGCAT
upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 14
-cttgttgtcattgattgatgtccttgagtctgtgaaggaaaacagctagtgctctgaaattttagctcgttggcatgaatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
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gtacgtacccattacttaccctacttatccaattatctgcacttcacctattct-tgaaagtgagactaacaaagacgtgttttaaaatgtttgt-tacagGTGTGTGTCTCAACGACAAACAGGAACTTCCCCGGTCGGATGGGACACAAAGAAGGGCAAATTTACTTAGCGTCTCCTTACACTGCTGCAGCCTCGGCTT
upper sequence: GRMZM2G010044_T01 (Zea mays), 3'ss of exon 13
lower sequence: EDO97224 (Chlamydomonas reinhardtii), 3'ss of exon 11
------cttgttgtcattgattgatgtccttgagtctgtgaaggaaaacagctagtgctctgaaattttagctcgttggcatgaatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
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ccggctcccggcgtccttagtccatgcaaccaatctcttctcactcacca--tacccccctgccgccgctgc-cgctggccctccgccgc--atgtggccgc-cagGTGTGCGTGTCCACCACCAACCGCAACTTCCCCGGCCGCATGGGCCACAAGGAGGGCCAGATCTACCTGGCCTCGCCCTACACCGCCGCCGCCTCCGCCCMapped 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|24769037|gb|CA404166.1|CA404166EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
EST:
gi|7162228|gb|AW519835.1|AW519835EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
EST:
gi|91051661|gb|EB162079.1|EB162079EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTTTGCGTGTCCACCCCGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
EST:
gi|7137997|gb|AW499377.1|AW499377EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
EST:
gi|86473276|gb|DY239646.1|DY239646EST: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACT GTTTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
genomic: CTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAG
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:
45 (upstream exon),
38 (downstream exon)
Score:
23GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
Block sizes:
45 (upstream exon),
48 (downstream exon)
Score:
89GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
Block sizes:
47 (upstream exon),
46 (downstream exon)
Score:
61GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
Block sizes:
43 (upstream exon),
45 (downstream exon)
Score:
24GATATTTGAGGAGGCTGGTTGTGACACACCAGCAAGTCCTAATTGTGGTGCTTGTTTGGGTGGCCCTCGTGATACATATGCACGGATGAATGAACCTACTgtaagtatct ... ggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagtgctctgaaattttagctcgttggcatgaatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
tggtaac putative branch site (score: 24)
tgaaatttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgttgtcattgattgatgtccttgagtctgtgaaggaaaacagctagtgctctgaaattttagctcgttggcatgaatctggtaacctggatgtgcagGTCTGCGTGTCCACCACGAACAGGAACTTTCCGGGCAGGATGGGCCACAAGGAAGGGCAAATCTACCTGGCGTCTCCCTACACTGCGGCTGCCTCAGCCC
-ttgttgt
- - - - - - -attgatg
- - - - - - - - - - - - - - - - - - - -aaacagc
- - - - - - - - - - - - - - - - - - - - - - - - -tgctctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgaa