Sequence
atgc intronic sequence ATGC exonic sequence...gaaatgtcaaaacgtcttataatttgaaattttggaacagagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os04g46620.1 (Oryza sativa), 3'ss of exon 11
-------------------------------------------------------------------------------------------------------------gaaatgtcaaaacgtcttataatttgaaattttggaacagagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
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gtatgcctcaccttttgtttatcgagttgtaaccacattggaatacataattgtgcagatgactaatagaattaataaatgatgaagcgacttcccttgcgatacccctgtaatttta----gtctta-agtttgttgcttctagtcctaatattaatgctacacca-actgtttggtgctgtcctaatttggtagtaaa---ttgcagGTATCTACATTTGCTGATATGGAAGGTGAAGAGACATTCGATTCATCGTTCCTTGGACATGCTGATGAAGTTGTTGAGGAAAGAATTGCTGATGATGATG
upper sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G12970.1 (Glycine max), 3'ss of exon 11
gaaatgtcaaaacgtcttataat-ttgaaattttggaacagagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaaccttt-cagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
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gcaacatcagtctcttgtatagtatcctcttttttggatagaagt--tttgaatactattttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
upper sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA05G29870.1 (Glycine max), 3'ss of exon 11
-gaaatgtcaaaacgtcttataat-ttgaaattttggaacagagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaaccttt-cagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
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agcaacatcaatctcttgtatagtatccactttttcggataga---agttttgaatactatttcctttatgtatcattggacttgatttttactttgacacagGTCTCAACATTTGCTGATATGGAAGGGGAGGAAACATTTGAACCATCTTTTCTTGGATATGCTGATGAGGTTGTTGAGGAGCGAATTTCTGATGATGCTG
upper sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT3G20050.1 (Arabidopsis thaliana), 3'ss of exon 11
gaaatgtcaaaacgtcttataatttgaaattttggaacagagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
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-----------gtacttcctgcgctaggctttttcaatacc-----catgttgtcaaac-----taaaatttcaactaatatatttatcctttattttagGTCACCACTTTTGCTGACATGGAGGGCGAAGAAACATTTGATCCAGCTCACCTTGGATCTGCTGATGAGGTTGTTGAAGAGAGAATCGCAGATGATGATG
upper sequence: GRMZM2G110626_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv15s0021g02230.t01 (Vitis vinifera), 3'ss of exon 11
gaaatgtcaaaacgtcttataatttgaaattttggaaca-gagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaaccttt-cagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
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-catggatattatgttatgctacttgtgcttatcttttatgatagtcaaagatacccaac-ttatcttgtttatcgttatgttacccttcgatgttctgcagGTTTCAACGTTTGCTGACATGGAAGGGGATGAGACATTTGATTCATCATTTCTTGGATATGCAGATGAAGTTGTGGAGGAACGCATTGCAGATGATGATGMapped 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|21331740|gb|BQ487121.1|BQ487121EST: TGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATG GTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
EST:
gi|31612209|gb|CD568831.1|CD568831EST: TGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATG GTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
EST:
gi|29130817|gb|CB381521.1|CB381521EST: TGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATG GTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
EST:
gi|211469891|gb|FL096480.1|FL096480EST: TGCGCAAGGWAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATG GTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
EST:
gi|211469889|gb|FL096478.1|FL096478EST: GCGCAAGGAAGA-TTGCGCCATTGTTGCCAAAGCCACTGGTGCAACTATG GTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
genomic: GCGCAAGGAAGATTTGCGCCA-TGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
EST:
gi|8103020|gb|AW927688.1|AW927688EST: TGCGCAAGGAAGATTTGTGCCATGTTGCCAAAGCCACTGGTGCAACTATG GTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTCGATTCATCATTC
genomic: TGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
EST:
gi|166536663|gb|EG262981.1|EG262981EST: TGGTGCAACTATG GTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
genomic: TGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTC
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),
42 (downstream exon)
Score:
132TACTTTGTTGAGGCTGGAGCTATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
Block sizes:
49 (upstream exon),
42 (downstream exon)
Score:
96TACTTTGTTGAGGCTGGAGCTATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
Block sizes:
49 (upstream exon),
49 (downstream exon)
Score:
85TACTTTGTTGAGGCTGGAGCTATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
Block sizes:
49 (upstream exon),
42 (downstream exon)
Score:
77TACTTTGTTGAGGCTGGAGCTATTGCAGTAAGGCGTGTGCGCAAGGAAGATTTGCGCCATGTTGCCAAAGCCACTGGTGCAACTATGgtaactgatt ... aacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcacgacagaaaacgttattaggatttaaggtagcttgacaattgaacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
gcttgac putative branch site (score: 77)
cctttc putative PPT
ttattaggatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaaatgtcaaaacgtcttataatttgaaattttggaacagagggagcacgacagaaaacgttattaggatttaaggtagcttgacaattgaacctttcagGTGAGTACATTTGCAGACATGGAAGGTGAAGAAACATTTGATTCATCATTCCTTGGACATGCTGATGAAGTTGTGGAGGAAAGAATTGCTGATGATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - gaacaga
- - - - - - - - - - - - - - - - - - - - - ggagcac
- - - - - - - - - - - - - - - - - - - - - - - - - acagaaa