Sequence
atgc intronic sequence ATGC exonic sequence...attttcaagaccatgtttgacagtgttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
Basic information
species | Glycine max |
transcript | GLYMA10G00880.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 4
----attttcaagaccatgtttgacagtgttagttttttggtgcattcg-gat---tatttaaattc---actttc----atctcatggatctcacagtgagtttgtatt----gccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
||| | | || || ||| || || | ||| ||||||||| |||| | |||| | | | ||| || | | |||||||| || || | | |||||| |||| ||||| |||| || || || |||||||||||||| ||||| ||||| |||||||||| |||||||||||
gtaagtttgttctttagaatctttcaccaataatttcttatcacaaacatgatacatatttaaatgttgggctttttcaaacttcattattgtgattcatcttttctactatctggcagATGCTAAAGTTCAAAGATAACAATATTAACAATGAGGGAATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 4
attttcaagaccatgtttgacagtgttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcaca-gtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
|| || ||||| | || | ||| || | | | || | |||| || | | ||| |||||||| ||||| | |||||| | || ||||| || | || || || |||||||||||||| ||||| ||||| |||||||||| |||||||||||
------------------------gtaagccttttgtcttgattc--ttttgtaagttgccctgaaattctttaatctaacccatctctactgtttggcagATGCTAAATTTCAAGGATAACAATATAAACAATGATGGGATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 2
attttcaagaccatgtttgacagtgttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
|| || ||||| || | || || | | || | |||| || | | ||||||||| || ||||| | | |||||| | || ||||| || | || || | |||||||||||||| ||||| ||||| ||||| |||| ||| |||||||
------------------------gtaagccttttgtcttgactcctttgt--aagtttcccagaaattcttttatctgaccatctctactatttgccagATTCTAAATTTCAAAGATAACAATATAAACAATGAGGGGATGCTTCGTATAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTCGGAGGATACCTTCTTT
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G433989_T01 (Zea mays), 3'ss of exon 1
attttcaagaccatgtttgacagtgttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
|| || ||||| || | || || | | | || | |||| || | | |||||||||||| ||||| | | |||||| | || ||||| || | || | || |||||||||||||| ||||| ||||| ||||| |||| ||| |||||||
------------------------gtaagccttttgtcttgactcctttgt--aagtttccctgaaattcttttatctgaccatctctactatttgccagATGCTAAATTTCAAAGATAACAATATAAACAATGAGGGGATGCTTCATACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTCGGAGGATACCTTCTTT
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 5
attttcaagaccatgtttgacagtgttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
|| || ||||| || | || || | | | || | |||| || | | ||| |||||||| ||||| | | |||||| | || ||||| || | || || || |||||||||||||| ||||| ||||| ||||| |||| ||| |||||||
------------------------gtaagccttttgtcttgactcctttgt--aagtttccctgaaattcttttatctgaccatctctactatttggcagATGCTAAATTTCAAAGATAACAATATAAACAATGAGGGGATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTCGGAGGATACCTTCTTT
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
attttcaagaccatgtttgacagt-gttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
|| | |||| ||| | || ||| | | | | | | | || ||||| | || || || ||||| ||||||| |||||| | ||||| | | || |||| ||||| ||| |||| ||||||||||||||||||||||||| || ||||||| |||||||||
--------------gtaaggcagttactagatcttatgtggaatagaggtgtgtg--tccatcttcatttactgatactattcatggaa----attgc-agATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTG
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 4
attttcaagaccatgtttgacagtgttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
|| ||| ||||| | || ||| | | |||| ||| ||| | | ||| |||| |||||||| || ||||| ||| | | ||| | ||||| ||| | | |||||||||||||| || || || ||||||||||||||||| || |||||
----------------------gtaagagtcttttgctcactttttatttctagtgataacttgtctctaatgattttt----tgactttg------cagATGCTTAACTTTTCGAACGATGTATTGAATGACGAAGGGAGATTAAGAACGGTTCTTGATGTCGGATGCGGAGTTGCGAGTTTTGGAGCTTACCTTCTCG
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: AT4G14360.1 (Arabidopsis thaliana), 3'ss of exon 4
attttcaagaccatgtttgacagtgttagttttttggtgcattcg-gattatttaaatt-cactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
| | |||| || || | | || | || ||| ||||||| | | | | || | || |||||||| || | | | |||||| || || || | ||||| || |||||||| | |||||||| |||||||||||||||||||||| |||||| | |
----------------gtaaggaagttacacttggtgtttgtacaagagaacgtatattattctttcatttgctaattgtattcttggaaat---ttttcagATGCTTAACTATCCTAACAACGTGCTGAACAACGGTGGAAGGCTAAGGACGGTTTTCGATGTTGGTTGTGGTGTTGCGAGTTTTGGAGGTTATCTTTTAT
upper sequence: GLYMA10G00880.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 4
attttcaagaccatgtttgacagtgttagttttttggtgcatt--cggattatttaaattcact------ttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
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-------atttcattttagggatttctggttctttggtaaattattttagtattttcttctactgcatggttgaagcaataattctatttgtg-gcttgtactggcagATGCTCAACTTTTCAAACAATAATCTAAACAACGGGGGAAGGATACGAACTGTTTTTGATGTTGGCTGTGGTGTTGCAAGTTTTGGAGCCTATCTTCTTTMapped 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|207701332|gb|GD683319.1|GD683319EST: GGACACATTTTCACAAAGGAGCTGACAAGTACATTGCATCAATTGCAAAT ATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACG
genomic: GGACACATTTTCACAAAGGAGCTGACAAGTACATTGCATCAATTGCAAATgtaagaggct ... gtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
atctcac putative branch site (score: 3)
tttaaattcacttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
attttcaagaccatgtttgacagtgttagttttttggtgcattcggattatttaaattcactttcatctcatggatctcacagtgagtttgtattgccagATGCTCAATTTTTCAAACAACAATCTTAATAATGAAGGAAGACTGCGGACGGTTCTTGATGTTGGCTGTGGTGTTGCGAGTTTTGGAGCATATCTTCTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA