Sequence
atgc intronic sequence ATGC exonic sequencegtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 9
gtctgat--ctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
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gtctgatgcctaaccacatgttg-aaatgctatacgttttctgccagttttagctaatttctt-tttctgcgttaatgcagGTTCATTTTTTCCGTCCGGTTCCCAAGGAATATCTTCATTCTGCAGAACTGAGAGATATCATGCAATTTGGGAGCAGCAATACCGCTGTTTTCTTTAAAA
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 11
---------gtctgatctca-ccatgcgatgg-aaacttcatattctttctgttaagtaaaactgatctt------gaat---ttatgcatgaatg-----cagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
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gtaagactaacatgatttaaattttaagattataaggtttaaaatttctttttaaaaacgaattgtgcttttaattgaatgtttttttaataaattattcccagGTCCATTTTTTCCGTCCCGTTCCAAAGGAATATATGCACTCTGCTGAATTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 14
--------------------gtctgatctcaccatgcgatggaaacttca-tattctttctgttaagtaa--aactgatcttgaatttatgcat--------------gaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
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gtatgactaaacaaaaaaataactagttaaactaaacattatatagtttactattacaattattaaaaaatgaactgtgcttttaattgtgttttttcttgatcaattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGCAATACTGCAGTCTTTTTTAAAA
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 11
----------------gtctgatctcaccatgcgatggaaacttcat-attctttctgttaagtaa--aactgatcttgaatttatgca----------------tgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
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gtatgactaaatgaaaaactagttaaactaaacattatatagtttatcattacaattattaaagaatgaattgtgcttttaattgtgtgccttttcttgatccattggctatagATTCATTTTTTCCGTCCAGTTCCTAAGGAATATTTGCACTCAGCTGAGTTGAGAGACATAATGCAATTTGGAAGCAGTAATACTGCAGTCTTCTTTAAAA
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 11
---------gtctgatctcaccatg-cgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgc---atgaatg-----cagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
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gtaatactaacatgattaaattttaacactataaggtttaaaacttctttttaaaaactaattg--tttgaattttttttcaataaattattcccagGTCCATTTTTTCCGTCCCATTCCAAAGGAATATATGCACTCTGCTGAGTTGAGGGACATAATGCAATTTGGAAGCAGCAATACTGCAGTATTTTTTAAAA
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: AT5G65930.1 (Arabidopsis thaliana), 3'ss of exon 8
------------------gtctgatctcaccatgcgatggaaact-tcatattctttctg---ttaagtaaa----actgatcttgaatttat-----gcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
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gttagtctcaatataaatgttatacattatgactttaaaaaaactgttattgttgtttggaattcaaatctatgttgttggatttgaatttgttgtttgctttcttgtagGTTCACTTTTTTCGACCGGTTCCTAAAGAATATCTGCACTCTGCTGAACTACGTGACATCATGCAATTTGGCAGCAGTAACACTGCTGTCTTTTTCAAAA
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 10
-------------------gtctgatctcaccatgcgatggaaacttcatattc----tttctgttaagtaaaactgatcttgaattta----tgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
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gtgagtcagagttatattattataatgtatctgtacattgcaaatttgatgtttgaattatagatctattgcaacagaacatgaatttgattgttcattctcacagGTTCATTTTTTCCGTCCAGTTCCAAAAGAGTATTTGCATTCTGCTGAACTAAGAGATATAATGCAATTTGGTAGCAGCAATACTGCTGTATTTTTTAAGA
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ30174 (Selaginella moellendorffii), 3'ss of exon 10
gtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
| | | | | ||||| ||| | | || | | || ||| | | |||||||| |||||||| ||||| || || |||||| | ||||| || || | |||||||||||||||||||| || |||||||| || || || |||||||
-----------gtacgtgcaagtatattcatgttcgctgttttga-----------catgtgtttcttaa------cagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTGAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAA
upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 10
lower sequence: EFJ06058 (Selaginella moellendorffii), 3'ss of exon 10
gtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
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-------------------------gtacgtgcaagtatattcatgttcg--cggttttga-catgtgtttcttaacagGTTCATTTTTTCCGGCCAGTACCTAAAGAATATTTACATTCGGCTGAGCTTAGAGACATCATGCAATTTGGAAGTAGCAATACCGCAGTGTTTTTTAAAAMapped 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|18383721|gb|BM416921.1|BM416921EST: GCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGG G-TCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
genomic: GCTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
EST:
gi|18649769|gb|BM498588.1|BM498588EST: CTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGG GTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
genomic: CTACCTGGAAAAATTATTCTGGGAATCAACAAACGAGGGgtctgatctc ... atgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
aactgat putative branch site (score: 3)
ttaagtaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgatctcaccatgcgatggaaacttcatattctttctgttaagtaaaactgatcttgaatttatgcatgaatgcagGTTCACTTTTTCCGTCCAGTTCCCAAGGAATATCTTCATTCTGCAGAATTAAGAGACATCATGCAATTTGGTAGCAGCAATACTGCTGTTTTCTTTAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT