Sequence
atgc intronic sequence ATGC exonic sequence...tttgcgctcctacttggtgctgttttttgtgcgacttctgcaggcgttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G069651_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g30412.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------------------------tttgcgct-cctacttggtgctgttt---tttgtgcgacttctgcaggcgttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
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gcgtgtaatctgtatagtgtggtagtgtgctgatgcttttacagatctgtgtgtttgggtgatgaattcgatgtgacatgggtgtgtgtggtttctgcagGCATTGGATAAGATTAGGTTCGAGAGCCTCACGGACAAGAGCAAGCTCGATGCGCAGCCGGAGCTGTTCATCCACATTGTCCCCGACAAGGCTAGCAACA---------------------------------------------------------
upper sequence: GRMZM2G069651_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S220_83V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------tttgcgctcctacttggt-gctgttttttgtgcgacttctg-caggcgttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
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ggacgtgccacaaaattgattgtcaacagcgaaacagtaatttatgcttgtatgactggagttggttctcatttgttactttacgcttgagccctggcagGCCTTGGACAAGATTAGGTTTGAGTCCCTAACCGACAAGAGCAAGATGGATGGGCAGCCCGAGCTGTTCATTCATATTGTTCCCGACAAGGCCAACAACA---------------------------------------------------------
upper sequence: GRMZM2G069651_T04 (Zea mays), 3'ss of exon 1
lower sequence: PP1S83_80V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------tttgcgctcctacttggtgctgttttttgtgcgacttctgc--aggcgttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
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tgtgtaggtttactttgaaatgtgccgtgatgtgtctacgtgtttgaaagggtgttgagtgttgttgccatcccctgaactgtatttgtcttatgtttagGCCCTGGACAAGATCCGCTTCGAGTCACTGACAGACAAGAGCAAGCTCGATGGCCAGCCAGAGCTCTTCATCCATATCATTCCCGACAAGGCGAACAATA---------------------------------------------------------
upper sequence: GRMZM2G069651_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ22362 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------tttgcg-ctcctacttggtgct---gttttttgtgcgacttctgcaggcgttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
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gtgagtgttagatgctcgttcggcgatatttcactgcgattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcgttctttctgcgatttc--cagGCTCTCGACAAGATTCGGTTCGAAGGGCTGACTGACAAGAGCAAGCTCGAGAGCCAGCCGGAGCTTTTCATCCACATCGTTCCGGACAAGGCGAGCAAGA---------------------------------------------------------
upper sequence: GRMZM2G069651_T04 (Zea mays), 3'ss of exon 1
lower sequence: EFJ25533 (Selaginella moellendorffii), 3'ss of exon 1
--------------------------------------------------------------tttgcg-ctcctacttggtgct---gttttttgtgcgacttctgcaggcgttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
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gtgagtgttagatgctcgttcggcgatattttactgctattctcatcgatctttgccttctttctgcgatttctcaccgatctttgcattctttctgcgatttc--cagGCTCTCGACAAGATCCGGTTCGAAGGGCTGACTGACAAGAGCAAGCTCGAGAGCCAGCCGGAGCTTTTCATCCACATCGTTCCGGACAAGGCGAGCAAGA---------------------------------------------------------Mapped 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|211125669|gb|FL192426.1|FL192426EST: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGAT CCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCC
genomic: ATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgc ... cgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
cactgac putative branch site (score: 2)
acaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgcgctcctacttggtgctgttttttgtgcgacttctgcaggcgttggacaaaatcaggttcgagagcctcactgacaagagcaagctcgatgcgcagCCGGAGCTGTTCATCCACATTGTACCAGACAAGGCTTCGAACACGCTCTCCATCATCGACAGCGGCATCGGCATGACCAAGTCCGACCTTGTCAACAACC
- - -gctccta
- - - - - - - -ggtgctg
- - - - - - - - - - - - - - - - - cttctgc
- - - - - - - - - - - - - - - - - - - - - - - - -gacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaagct