Sequence
atgc intronic sequence ATGC exonic sequencegtatcatgcttttactctgtctgagttgattaatggtgtgcttatctttaatgatctcttctgaaccttgttttttactgggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCTAGTTTACCCTATGGCTGGAGTAGATAT
Basic information
species | Glycine max |
transcript | GLYMA14G04890.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g30540.1 (Oryza sativa), 3'ss of exon 3
-----gtatcatgcttttactctgtctga----------gttgattaatggtgtgctt--atctttaatgatctct-tctgaaccttgttttttactgggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCTAGTTTACCCTATGGCTGGAGTAGATAT
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gtaacatatctcgcggtcgcggttcctagtggaaatgcggttaccttgggacttgcttgaagcgcggagggttttgatatagatgttctgcctttgcgtgtagGCGTGTGCTGATTTTCCCTAAGGGGAACAATGTGGACCATTTCTCTATGTATTTGGATGTCGCGGACTCGGTGAATCTCCCTTATGGATGGAACCGGTAT
upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G014805_T01 (Zea mays), 3'ss of exon 3
------------gtatcatgcttttactctgtctgagttgatt-aatggtgtgcttatctttaatgatctcttctgaacct--tgttttttactgggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCTAGTTTACCCTATGGCTGGAGTAGATAT
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gtgagcttttggatctcttctcttgccactgtaactgctgacggaaacatgggtaaatgtttggtgggttttaatggatgtgctactttttgcttg-cagGCGTGTCCTAATTTTCCCCAAGGGGAACAATGTGGATCACTTCTCGATGTATTTGGATGTTGCAGATTCTGGGAACCTCCCATACGGGTGGAGCCGGTAT
upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G426486_T01 (Zea mays), 3'ss of exon 4
-------gtatcatgcttttactctgtctgagttgattaatg-gtgtgcttatctttaatgatctcttctgaacct--tgttttttactgggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCTAGTTTACCCTATGGCTGGAGTAGATAT
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gtgaccttttggatcccttgccactgtgaccgctactggaagcatgggtagatgtctggagagttttaatggacgtgctactttttgcttg-cagGCGTGTGCTAATTTTCCCCAAGGGGAACAATGTGGATCACTTATCGTTGTATTTGGATGTTGCGGATTCTGGGAGCCTCCCATATGGGTGGAGCCGGTAT
upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G551402_T01 (Zea mays), 3'ss of exon 1
---------gtatcatgcttttactctgtctg----agttgattaatggtgtgcttatctttaatgatct--------cttctgaaccttgttttttactgggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCTAGTTTACCCTATGGCTGGAGTAGATAT
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gtgagctccttatccttccactgttctgcctgcagaaaccatggagttttttccctagcccctctgttctttagagtactcataacatctgttgaccttcatgcagGAGTGTGCTGATTTTCCCCAAGGGGAACAATGTGGACCACTTCTCAATGTACTTGGATGTTGCTGACTCAACCAGCCTTCCGTATGGTTGGAGCCGCTAT
upper sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------------------------------gtatcatgctt-ttactctgtctgagttgattaatggtgtgcttatctttaat--gatctcttctgaaccttgttttttact-gggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCTAGTTTACCCTATGGCTGGAGTAGATAT
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gtattttaattttttttcatccaaaatggcattattgttattattattatcatcatcatcttcattattattattgttgttgttgctataaccattattcttcatatggctagtgccaatcctcataattgatttgaacagGCGGGTGCTTATTTTTCCAAAGGGAAACAATGTTGAACATTTGTCTATGTACTTGGATGTTGCGGATTCATCAAGTTTGCCCTATGGGTGGAGTAGATATMapped 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|208269856|gb|GE072180.1|GE072180EST: AATACAAAGAAGCTCTATTCAGAAATATTTGTTGTTGGTGGTTATAAATG GCGTGTACTTATTTTCCCAAAAGGGAACAATGGGGACTATTTGTCCATGTA
genomic: AATACAAAGAAGCTCTATTCAGAAATATTTGTTGTTGGTGGTTATAAATGgtatcatgct ... tactgggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taatggtgtgcttatctttaatgatctcttctgaaccttgttttttactgggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCTAGTTTACCCTATGGCTGGAGTAGATAT
ctttaat putative branch site (score: 4)
ccttgttttttact putative PPT
ttatctttaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatcatgcttttactctgtctgagttgattaatggtgtgcttatctttaatgatctcttctgaaccttgttttttactgggcagGCGTGTACTTATTTTCCCAAAAGGGAACAATGTGGACTATTTGTCCATGTATTTGGATGTTGCAGATTCAGCTAGTTTACCCTATGGCTGGAGTAGATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA