Sequence
atgc intronic sequence ATGC exonic sequencegtataacttttggtgctattgattttatttgttagtaaatgtgaaactcttttattttgctaacaaggaactcatcatttttcagATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGCAGTATATGACAGTCCTGAAGATGTCCCGGAAGAT
Basic information
species | Glycine max |
transcript | GLYMA08G45990.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G079256_T01 (Zea mays), 3'ss of exon 4
--------------------gtataacttttggtgctattgattttatttgttagtaaatgtgaaactcttttattttgctaacaaggaactcatcatttttcagATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGCAGTATATGACAGTCCTGAAGATGTCCCGGAAGAT
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gtgagtgcattaacagtagtttgaggctttgagcataattgaagtttcctttattccacttcagtgtttcttgatcgaactgatgttatccttttgactttacagGCTACCTGATGGATCTCTTATGGAGATTGCTAAAGTATATCCACTGGACGCAGTTTATGACACCCCTGAGGATGTTCCTGAAGAT
upper sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g01310.t01 (Vitis vinifera), 3'ss of exon 4
-------gtataacttttggtgctattgattttatttgttagtaaatgtgaaactcttttattttgctaacaaggaactcatcatttttcagATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGCAGTATATGACAGTCCTGAAGATGTCCCGGAAGAT
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gtaagatgttagacttaggtttctgtcaaatttaaatgggaataaaca-aaaagtgggctcttctgat-----ggaatgtttaatgttttagGTTGCCAGATGGTTCTTTGATGGAGATCACCAAAATATATCCTTTGGATGCAGTTTATGACACCCTTGAGGATGTACCTGAAGAT
upper sequence: GLYMA08G45990.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S29_256V6.1 (Physcomitrella patens), 3'ss of exon 3
----gtataacttttggtgctattgattttatttgttagtaaatgtgaaactcttttattttgctaa-caaggaactcatca----------tttttcagATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGCAGTATATGACAGTCCTGAAGATGTCCCGGAAGAT
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tcccgtactgtttgcacgcgtattttgtcagggtattataggatctgtatttgatgtacttggtaaatcccgcatcttatcgctgtagttgtttccttagGCTTCCCACCGGAGGATTACTCGAGATTGCCAAAGTGTATCCCTTAGATGCTGTATTCGACACTCCTGAAGATGTGCCTGAGGATMapped 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|8283272|gb|BE020833.1|BE020833EST: AATATATTTGAGTCCAGTCTACGACGTGGAAAATTTGACGAGTCACGCAA ATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGC
genomic: AATATATTTGAGTCCAGTCTACGACGTGGAAAATTTGACGAGTCACGCAAgtataacttt ... catttttcagATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttagtaaatgtgaaactcttttattttgctaacaaggaactcatcatttttcagATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGCAGTATATGACAGTCCTGAAGATGTCCCGGAAGAT
tgctaac putative branch site (score: 1)
tcatttttc putative PPT
aaactcttttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataacttttggtgctattgattttatttgttagtaaatgtgaaactcttttattttgctaacaaggaactcatcatttttcagATTACAAGATGGTTCATTGATGGAGATTGCTAAAGTGTATCCTTTGGATGCAGTATATGACAGTCCTGAAGATGTCCCGGAAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA