Sequence
atgc intronic sequence ATGC exonic sequence...tacgcattcatgaaattacactcactaacgttttagagtgaatgaaaaagaagtactgtaaatgaatttaacgaaacgtgatttcgtggtgtacttgcagGGTTACGGGATGACAGAGGCAGGGCCAGTGCTATCAATGTGCTTAGCGTTTGCGAAGGAGCCAATGCAGGTGAAATCAGGTGCCTGCGGGACTGTCGTAA
Basic information
species | Glycine max |
transcript | GLYMA17G07180.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G07180.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g34790.1 (Oryza sativa), 3'ss of exon 1
tacgcattcatgaaattacactcactaacgttttagagtgaatgaaaaagaagtactgtaaatgaatttaa--cgaaacgtgatttcgtggtgtacttgcagGGTTACGGGATGACAGAGGCAGGGCCAGTGCTATCAATGTGCTTAGCGTTTGCGAAGGAGCCAATGCAGGTGAAATCAGGTGCCTGCGGGACTGTCGTAA
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---gtataacccaaactagacgaacacaaggaccaaatcaaacaataaaaa----caacaacaacatccaagtggaaatttgatgtgaatttgatcgagcagGGGTACGGGATGACGGAGGCAGGGCCGGTGCTATCAATGTGCATGGCGTTCGCGAAGGAGCCGACGCCGGTGAAGTCCGGCGCGTGCGGCACGGTGGTGC
upper sequence: GLYMA17G07180.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g08100.1 (Oryza sativa), 3'ss of exon 2
tacgcattcatg--aaattacactcacta-acgttttagagtgaa---tgaaaaagaagtactgtaaatgaatttaacgaaacgtgatttcgtggtgtacttgc------agGGTTACGGGATGACAGAGGCAGGGCCAGTGCTATCAATGTGCTTAGCGTTTGCGAAGGAGCCAATGCAGGTGAAATCAGGTGCCTGCGGGACTGTCGTAA
||| ||| | |||||| ||| | || | | || | | | | | | | | || | || | | ||| | | | | | |||||||||| ||||| ||||| ||||||||||| |||||||| | |||||||| |||||||| | |||| || || || | ||||| || || ||
-gtaaattgatgccacattacaatcattgcgcggacgaaaacaaaatctcctctctctctctttttttttgagtcactgacaagttagtccgtcatatcccttcttctttagGGTTACGGTATGACTGAGGCTGGGCCAGTGCTGGCAATGTGCCTGGCGTTTGCCAAGGAGCCCTTCAAGGTTAAGTCCGGGTCGTGCGGTACAGTGGTGC
upper sequence: GLYMA17G07180.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g14760.1 (Oryza sativa), 3'ss of exon 1
tacgcattcatgaaattacactcactaacgttttagagtgaatgaaaaagaagtactgtaaatgaatttaacga--aacgtgatttcgtggtgta---cttgcagGGTTACGGGATGACAGAGGCAGGGCCAGTGCTATCAATGTGCTTAGCGTTTGCGAAGGAGCCAATGCAGGTGAAATCAGGTGCCTGCGGGACTGTCGTAA
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-----agatatcaaattagtcctacaaaaatgttatattctaagcatgtccagctaattaagcaaatgtggtgatgatctttgctgcccactatgtggcattcagGGGTATGGAATGACTGAGGCAGGGCCAGTGCTGTCAATGTGCCTAGCATTCGCCAAGGAGCCCTTCAAGGTGAAGTCCGGTGCGTGCGGGACGGTGGTGC
upper sequence: GLYMA17G07180.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G048522_T02 (Zea mays), 3'ss of exon 2
------------------tacgcattcatgaaattacactcactaacgttttaga-gtgaatgaaaaagaagtactgtaaatgaatt-taacgaaacgtgatttcgtggtgtacttgcagGGTTACGGGATGACAGAGGCAGGGCCAGTGCTATCAATGTGCTTAGCGTTTGCGAAGGAGCCAATGCAGGTGAAATCAGGTGCCTGCGGGACTGTCGTAA
|| || |||| | | | | | | | ||| ||| | | ||| | | ||||| ||| | | | | |||||||| ||||||||||||||||| || ||||| || |||||| | |||||||| |||||||| ||| |||||| || ||||||||||| || || || |
gtgtgcctgccttctgcctagcagaacacgaaagttc-ccctccagctcgctagtcgtggctcgtgagttgacgac-taattaagccgcgttgaaacttgactaatcgtttga---acagGGTTATGGGATGACAGAGGCAGGCCCGGTGCTCTCGATGTGCATGGCGTTTGCCAAGGAGCCGTTGCCGGTGAAGTCCGGTGCCTGCGGCACGGTGGTGA
upper sequence: GLYMA17G07180.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S20_346V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------tacgcattcatgaaattac-----actcactaacgttttagagtgaatgaaaaagaagtactgtaa---atgaatttaacgaaacgtgatttcgtggtgta---cttgcagGGTTACGGGATGACAGAGGCAGGGCCAGTGCTATCAATGTGCTTAGCGTTTGCGAAGGAGCCAATGCAGGTGAAATCAGGTGCCTGCGGGACTGTCGTAA
| || | | | ||| | | || || | ||| ||| | | | || | | | | | ||| || || | | | | ||| |||||||||||||| |||||||| || || ||||||||| ||||||| || || || || ||| ||| | | ||||| |||| | || || || |||||
gtatcaaaacaatcgatgcaaacatttcccctttgtaatgcctacgtaaaagaagcaggagcataccaagttcatagcgtgtgc-acattgttgtccaggagcccacagacttatgtaagtttggtgttgggttgtgaattttgcagGGTTACGGAATGACAGAAGCTGGTCCAGTGCTAGCAATGTGTTTGGCATTCGCCAAGACTCCATTTCCAGTGAAGCCAGGGTCATGTGGTACAGTCGTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagaagtactgtaaatgaatttaacgaaacgtgatttcgtggtgtacttgcagGGTTACGGGATGACAGAGGCAGGGCCAGTGCTATCAATGTGCTTAGCGTTTGCGAAGGAGCCAATGCAGGTGAAATCAGGTGCCTGCGGGACTGTCGTAA
atttaac putative branch site (score: 3)
tgtaaatgaatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacgcattcatgaaattacactcactaacgttttagagtgaatgaaaaagaagtactgtaaatgaatttaacgaaacgtgatttcgtggtgtacttgcagGGTTACGGGATGACAGAGGCAGGGCCAGTGCTATCAATGTGCTTAGCGTTTGCGAAGGAGCCAATGCAGGTGAAATCAGGTGCCTGCGGGACTGTCGTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- -gcattca
- - - - - - - - - cactcac
- - - - - - - - - - - - - - - - - - - tgaatga
- - - - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacgaaac