Sequence
atgc intronic sequence ATGC exonic sequencegtgaaaatttgctaagagtatatgtgatcttcaatatactctctgatactgatgtaattgttgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
Basic information
species | Glycine max |
transcript | GLYMA20G35120.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 3
--------------gtgaaaatttgctaagagtatatgt--gatcttcaatatactctctgatactg-atgtaattg---ttgtttatat-aatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
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tctgttccgtccaatctatgcctttcaaaaaaaatgttttcaagtgctaatgtcctatcct-tactacacctcattggactcataaaaattgactttgcagGTTCCCATAAAATGGCCAAAAAGTCGTGATATTGTGTGGAAAGCAAATATTCCGCACACTCACCTTGCACATGAGAAGTCAGACCAGAATTGGATGATTG
upper sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 3
---------------gtgaaaatttgctaagagtatatgtgatcttcaatatactct--ctgatactgatgtaattgt---tgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
||| | ||| || ||| || | | | ||| || | |||| | | || | || ||||||||||| || |||||| |||| | |||| |||||||||||||| || ||||| |||||||||||| | |||||||| |||||||| |||||| ||
ggtttaacacgtccactgaccttccactatatactcatctgaaattagttctgtttgaatggatccttgctgagttgtatcagatccactattttttcagGTTCCTATAAAATGGCCAAAAAGTCGTGATGTAGTGTGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 1
----------------------gtgaaaatttg--ctaagagtatatgtgatcttcaatatactctctgatactgatgtaattgttgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
||| | |||| | || | || | || || |||| | |||| | | || | | || ||||| || || || |||||| |||| | |||| || ||||||||||| || ||||| |||||||||||| | |||||||| |||||||| |||||| ||
taataacacgtgccctgacagactgaccttccaatctaaaattagttctgtttgattgcatccttgctga----gctgtatccgatccacatttttttttccagGTCCCCATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 4
--------------gtgaaaatttgctaagagtatatgtgatc--ttcaatatactctc--tgatactga--tgtaattgttgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
||| | || ||| || || ||| | | | | | |||| |||| | | | | || ||||| ||||| || |||||| |||| | |||| || ||||||||||| || ||||| |||||||||||| | |||||||| |||||||| |||||| ||
taataacacgtgccctgacagactgaccttcctatctgaaattagttctgtttgattgcatccttgctgagctgtatccgacccacaattttttttccagGTCCCTATAAAATGGCCAAAAAGTCGTGATGTAGTATGGAAAGCAAACATTCCACACACTCACCTTGCAAAAGAGAAGTCAGACCAGAACTGGATGGTTG
upper sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgaaaatttgctaagagtatatgtgatctt--caatatactctctgatactgatgtaattgttgtttat---ataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
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----gtgtctatcgatatgttatacagttttatcgatatgattagttacgatgacataactgttttctcttccaatatgttttagGTTCCGATTAAATGGCCAAAAAGCAGAGATGAAGTGTGGAAAGTGAACATACCTCATACTCATCTTGCACATGAGAAGTCTGACCAAAACTGGATGGTTG
upper sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------gtgaaaatttgctaagagtat--atgtgatcttcaatatactctct-gatactgatgtaattgttgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
| |||||| || | || | || | || | | ||| |||| || | | | |||| | || | ||||||||||||||||||| | || |||||||| |||||||||||||| || || || |||||||||||| | ||||||||||| ||||| |||||| ||
gtgctatatttgctttcttgttttgctttgatttgtgattggttcctggttacattgtcttgatattgttttgttctttgtattgatttgcgtttagGTTCCTATTAAGTGGCCTAAGAGTAGAGATGAAGTGTGGAAAGCAAACATACCTCACACTCACCTTGCAAAAGAGAAGTCTGATCAGAACTGGATGGTTG
upper sequence: GLYMA20G35120.4 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0049g01180.t01 (Vitis vinifera), 3'ss of exon 3
gtgaaaatttgctaagagtatatgtgatcttcaatatactctctgatactgatgtaattgt-tgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
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gtgagaatgtgcgtaagcttaatagtaacaagggtgt----tgaagttttcttatttttgtgtgtgtctcttcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATACCTCATACTCACCTTGCACATGAGAAATCTGACCAGAATTGGATGGTTGMapped 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|254314767|gb|GR829760.1|GR829760EST: CTGCGGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCAGGATACAAG GTTCCTATTAAGTGGCCACAAAGCAGAGATGA
genomic: CTGCGGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCAGGATACAAGgtgaaaattt ... aatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGA
EST:
gi|6566784|gb|AW234416.1|AW234416EST: CTGCGGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCAGGATACAAG GTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATC
genomic: CTGCGGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCAGGATACAAGgtgaaaattt ... aatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcttcaatatactctctgatactgatgtaattgttgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
tactgat putative branch site (score: 2)
atgtaattgttgttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgaaaatttgctaagagtatatgtgatcttcaatatactctctgatactgatgtaattgttgtttatataatgttgcagGTTCCTATTAAGTGGCCACAAAGCAGAGATGAGGTGTGGAAAGCAAATATCCCACATACTCACCTTGCACACGAGAAGTCTGACCAGAATTGGATGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT