Sequence
atgc intronic sequence ATGC exonic sequencegtatctcttgtattgatagtttctactgatttaatagacaaaattgcttgcatcatttgataactgatttctttattttttcttttcctttatgtgttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTAGTATTACTTACGCTGCTTCAGTTGTATTCAATTTCTATGGTGGATGTCT
Basic information
species | Glycine max |
transcript | GLYMA04G09230.1 |
intron # | 20 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G09230.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os01g09246.1 (Oryza sativa), 3'ss of exon 19
gtatctcttgtattgatagtttctactgatttaatagacaaaattgcttgcatcatttgataactgatttctttattttttcttttcctttatgtgttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTAGTATTACTTACGCTGCTTCAGTTGTATTCAATTTCTATGGTGGATGTCT
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--------------gtttttctctgcca--ttattacataagactctt---atgataaaattcctggcatttgcacttaccataattctcttgttcttaaatgcagGATCTTGTTGGCTTAGTAATCTCAATATTGCTTCTCGCAGATTTTAGCTTAGTGTTACTGACTTTTCTCCAGCTATATTCATACTCTATGGCCGATGTTC
upper sequence: GLYMA04G09230.1 (Glycine max), 3'ss of exon 20
lower sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 17
gtatctcttgtattgatagtttctactgatttaatagacaaaattgcttgcatcatttgataactg-atttctttattttttcttttcctttatgtgttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTAGTATTACTTACGCTGCTTCAGTTGTATTCAATTTCTATGGTGGATGTCT
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gtgacttccattttgcacagctatcctgacatcattgcaacccctagtttggttatgatggatctacacaatcttgaacttaccaaggttctttttctttcctgcagGATCTTGTTGGTTTGGTGATCTCTATATTGCTTCTTGCAGATTTCAGCTTAGTATTGCTTACTTTTCTCCAGCTATATTCATATTCTATGATCGATGTGT
upper sequence: GLYMA04G09230.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM5G820781_T01 (Zea mays), 3'ss of exon 4
gtatctcttgtattgatagtttctactgatttaatagacaaaattgcttgcatcatttgataactgatttctttattttttcttttcctttatgtgttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTAGTATTACTTACGCTGCTTCAGTTGTATTCAATTTCTATGGTGGATGTCT
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--gtctttctctgccattgttcctgtccacagaataatta---ttaatctcttcattttgtg-ctgatct------tggttctgttc---------ttaactgcagGATCTTGTTGGTCTGGTAATCTCAATACTGCTTCTTGCAGATTTCAGCTTAGTTTTGCTTACTTTTCTCCAGCTGTATTCGTATTCTATGGTCGATGTTC
upper sequence: GLYMA04G09230.1 (Glycine max), 3'ss of exon 20
lower sequence: GRMZM2G412234_T01 (Zea mays), 3'ss of exon 9
--gtatctcttgtattgatagtttctactgatttaatagacaaaattgcttgcatcatttgataactgatttctttattttttcttttcctttatgtgttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTAGTATTACTTACGCTGCTTCAGTTGTATTCAATTTCTATGGTGGATGTCT
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gtctttctctgccactgttactgtccacagagtgattatg---aatcagtt-cattttgtgctgaatgctgatcttggttctgttgaac---------ttaactgcagGATCTTGTTGGTTTGGTAATCTCAATACTGCTTCTTGCAGATTTCAGCTTAGTTTTGCTTACTTTTCTCCAGCTGTATTCATATTCTATGGTCGATGTTCMapped 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|193590975|gb|FK546836.1|FK546836EST: TTTATCTTCTCTCTTTTATACTTCAGAATACAAAACCTGTTGGGCATCAG GATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTA
genomic: TTTATCTTCTCTCTTTTATACTTCAGAATACAAAACCTGTTGGGCATCAGgtatctcttg ... ttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcatttgataactgatttctttattttttcttttcctttatgtgttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTAGTATTACTTACGCTGCTTCAGTTGTATTCAATTTCTATGGTGGATGTCT
tttctttattttttct CT-rich tract
ataactgatttcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatctcttgtattgatagtttctactgatttaatagacaaaattgcttgcatcatttgataactgatttctttattttttcttttcctttatgtgttgcctgcagGATCTTGTTGGTCTAGTAATATCAATGTTGCTTCTAGGAGATTTTAGTTTAGTATTACTTACGCTGCTTCAGTTGTATTCAATTTCTATGGTGGATGTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA