Sequence
atgc intronic sequence ATGC exonic sequencegtaatccccgatttcccctcgtgcgttgatttcaacaagcttatcattaccaatttttagggttttttcttgatgttgcggtagcagttttttcatcgtattgatttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
Basic information
species | Glycine max |
transcript | GLYMA01G36990.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g13970.1 (Oryza sativa), 3'ss of exon 1
gtaatccccgatttcccctcgtgcgttgatttcaacaagcttatcattaccaatttttagggttttttcttgatgttgcggtagcagttttttcatcgtattgatttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
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-----------gttcgccgcgcagctcgccgccctccctcccacag--atcgatttcgccgagctctgattcacttatttatcgctttttttgcgtggctcccctctcc---gcagGCGACGATGATCTGCATAGACAACTCGGAGTGGATGCGGAACGGCGACTACTCGCCGTCGCGATTCCAGGCTCAGGCCGACGCCGTCAACCTCATCTGTG
upper sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G165926_T01 (Zea mays), 3'ss of exon 1
gtaatccccgatttcccctcgtgcgttgatttcaacaagcttatcattaccaatttttagggttttttcttgatgttgcggtagcagttttttcatcgtattgattt-cttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
| | ||| || | || || | || | | || | | | |||||| ||| ||| | | ||||| ||||||||||| || |||||||| ||||||||||| ||||| || ||| |||| || || || || || || || || || || || ||||| ||||
-----------------------------gtacgacatgcgccctgctgccgtttctcgctccgagaactccg-atccc--taactaatctcccatcgtgttggttttcctttgcagGCAACGATGATCTGCATAGACAATTCGGAATGGATGCGGAACGGCGACTACGCTCCGTCGCGGTTCCAGGCGCAGGCCGATGCCGTCAACCTCATCTGCG
upper sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 1
gtaatccccgatttcccctcgtgcgttgatttcaacaagcttatcattaccaatttttagggttttttcttgatgttgcgg-tagcagttttttcatcg----tattgattt-cttcaa-------cagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
| | || | | | | || | | ||| || | ||| |||| | |||| | | | | | ||||| ||| || | || |||| | ||| |||||||| |||||||||||||||||||| ||||||||||| || || ||||| ||||| || ||||||| |||||||| ||||| || ||||| || || |
-----gtatgcctatcctatttacttccacttttgccattctat--ttcctaatatttatactctttttcttctttcacaaattagggttttctcaccgattattttaatttgcatcattctgattcagGCGACTATGATCTGTATCGACAATTCCGAATGGATGCGAAATGGCGATTATTCTCCCACTAGATTTCAGGCTCAAGCCGACGCCGTTAATCTTATCTGTG
upper sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S14_318V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaatccccgatttcccctcgtgcgttgatttcaacaagcttatcattaccaatttttagggttttttcttgatgttgcggtagcagttttttcatcgtattgatttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
| ||| | | || ||||||| | | | | | |||||| | | | ||| || ||| ||| | | ||| | | | || ||||||||| ||| |||| || ||||| || || |||||||| ||||| ||||| || ||| || | |||||||||||||| || ||| | || || |||||||
---gtttgtttttttcgttactgagttgattgagggagcactgtgcgtgc--atttttgg------tgggtagagtt--ggaagctgttgaa-cgttatatgggtgtttt--acagGCGACCATGGTCTGCATGGACAACTCAGAGTGGATGCGGAACGGCGATTATTCACCTACTAGGTTTCAAGCTCAAGCTGATGCTATAAACCTGATTTGCG
upper sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ17485 (Selaginella moellendorffii), 3'ss of exon 1
gtaatccccgatttcccctcgtgcgttgatttcaacaagcttatcattaccaatttttagggttttttcttgatgttgcggtagcagttttttcatcgtattgatttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTC---TCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
| || ||| || | ||| | || || | | ||||||||||||||||| || |||||||| || |||||||| || || || |||| ||| | | |||| || | ||||| || ||||| ||||| || |
----------------------------------------------------------gtaagctcctcgcgatctttca-cgccaggcctatcttc--------tcttgtgccagGCGACGATGATCTGCATAGACAATTCCGAGTGGATGCGAAATGGGGACTACTATCCGACGAGTAGATTCCAGTCCCAAGCTGATGCTGTCAATCTTATCT---
upper sequence: GLYMA01G36990.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ28815 (Selaginella moellendorffii), 3'ss of exon 1
gtaatccccgatttcccctcgtgcgttgatttcaacaagcttatcattaccaatttttagggttttttcttgatgttgcggtagcagttttttcatcgtattgatttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTC---TCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
| || ||| || | ||| | || || | | ||||||||||||||||| || |||||||| || |||||||| || || || |||| ||| | | |||| || | ||||| || ||||| ||||| || |
----------------------------------------------------------gtaagctcctcgcgatctttca-cgccaggcctatcttc--------tcttgtgccagGCGACGATGATCTGCATAGACAATTCCGAGTGGATGCGAAATGGGGACTACTATCCGACGAGTAGATTCCAGTCCCAAGCCGATGCTGTCAATCTTATCT---Mapped 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|151394320|gb|EV264191.1|EV264191EST: ACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTAC
genomic: ACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatccccg ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTAC
EST:
gi|6069798|gb|AW099406.1|AW099406EST: CAACAATGGTGCTCGAG GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTAC
genomic: CAACAATGGTGCTCGAGgtaatccccg ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTAC
EST:
gi|207777270|gb|GD750451.1|GD750451EST: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAG GCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTAC
genomic: CAAACTTCTTTCACTCTTTCGCTTCTGAATCTTCAACAATGGTGCTCGAGgtaatccccg ... tcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttttcttgatgttgcggtagcagttttttcatcgtattgatttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
tattgat putative branch site (score: 3)
tttcttc CT-rich tract
ttttttcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatccccgatttcccctcgtgcgttgatttcaacaagcttatcattaccaatttttagggttttttcttgatgttgcggtagcagttttttcatcgtattgatttcttcaacagGCGACGATGATCTGTATCGACAATTCTGAATGGATGCGTAACGGTGATTACTCTCCTTCTCGATTTCAAGCTCAAGCAGACGCTGTGAATCTCATTTGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA