Sequence
atgc intronic sequence ATGC exonic sequencegttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
Basic information
species | Glycine max |
transcript | GLYMA14G40320.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 4
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
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--------------------------------------gtaatttcaatgtcgagagaccatttttcttttgtctggcatcat--atcttgctttagacttgggcttgatggcatctgatatatgcttatgc---agATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT
upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110574_T01 (Zea mays), 3'ss of exon 8
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
|| | ||| | || | | | | | |||| ||| | | | | | | || ||| | ||| |||||||||||||||| || |||||||| ||||| ||||| || || ||||| |||||||| ||||| ||| | || ||||| | || || || || ||||
-------------------------------------------gtagatttcaatgttgagagctgtttttttttctgttgggcaacgctttagaatcag-acctcaaggc--atctggtctatgcttatgc---agATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT
upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 4
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
|| | ||| | || | | | | | |||||||| | | | | | | || | ||| | ||| |||||||||||||||| || |||||||| ||||| ||||| || || ||||| |||||||| ||||| ||| | || ||||| | || || || || ||||
-------------------------------------------gtagatttcaatgttgagagctgtttttttttctgttgggcaatgctttagaatcagacctcaaggcatcaaatc---tatgcttatgc---agATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT
upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G022909_T01 (Zea mays), 3'ss of exon 5
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
|| | ||| | || | | | | | |||| ||| | | | | | | || ||| | ||| |||||||||||||||| || |||||||| ||||| ||||| || || ||||| |||||||| ||||| ||| | || ||||| | || || || || ||||
-------------------------------------------gtagatttcaatgttgagagctgttt---tttttgttgggcaacgctttagaatcag-acctcaaggc--atctggtctatgcttatgc---agATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT
upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G063988_T02 (Zea mays), 3'ss of exon 11
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
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-------------------------------------------gtagatttcaatgttcagagctgttttttttctgt-tgggcaacgctttagaatcag-acctcaaggc--atctggtctatgcttatgc---agATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTTGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT
upper sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaa--ctaaacttaaacatgttggtgc--tacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
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------------------------------------------------gttagttaatattactgttgtaaaaattttgta---ttttcttgtttataatttttctgacagtttgaattcttataatatgataaaatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATMapped 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|193549037|gb|FK507866.1|FK507866EST: CGGATAAGGAGGTGTTGGGAGAAGGTGATAACACCAAGCTTGATATTCAG ATTAAGTTGGACAAGGAAAAAGAAAATTCT
genomic: CGGATAAGGAGGTGTTGGGAGAAGGTGATAACACCAAGCTTGATATTCAGgttagtattg ... ggtgctacagATTAAGTTGGACAAGGAAAA-GAAAATTCT
EST:
gi|193513896|gb|FK466502.1|FK466502EST: ATAAGGAGGTGTTGGGAGAAGGTGATAACACCAAGCTTAGAATAATTCAG ATTAAGTTGGACAAGGAAAAGAAAATTCT
genomic: ATAAGGAGGTGTTGGGAGAAGGTGATAACACCAAGCTT-GA-TA-TTCAGgttagtattg ... ggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCT
EST:
gi|193681953|gb|FK622561.1|FK622561EST: CGGATAAGGAGGTGTTGGGAGAAGGTGATAACACCAAGCTTGATATTCAG ATTAAGTTGGACAAGGAAAAAGAAAATTCT
genomic: CGGATAAGGAGGTGTTGGGAGAAGGTGATAACACCAAGCTTGATATTCAGgttagtattg ... ggtgctacagATTAAGTTGGACAAGGAAAA-GAAAATTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
aactaaa putative branch site (score: 2)
tgttttattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtattgctatattctgattattatgcttttttttttaaggttgtttttggctatatgatttttatgaatacagtctaagcaatgctggtgttttattgttttggaactaaacttaaacatgttggtgctacagATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATCGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCGAAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA