Sequence
atgc intronic sequence ATGC exonic sequence...tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgttgtatatgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
Basic information
species | Glycine max |
transcript | GLYMA13G20980.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
-----tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgttgtatatgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| | | ||| ||| | ||| | | ||| ||||| | ||| | || |||| | | | || || | ||| ||||||||||| ||| ||||||||||||||||||| || |||||||| || || |||||||| ||| || ||||| | ||||||||||| || |||||
taccttttttcttttctttttattcttatttctagcttatagttctct-tctttctgtcacacacctaaaatggccattgt-tcttatttt---attttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------tacatagtaaggaaccattgttacagccccctttttttcttctctctt----------------ttcctttcacttt--gcatgtgattgttgtatatgaccttg-tgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| | | ||| | ||||| |||||| | | |||| | ||| || | || | | | | | | ||| | || ||| || |||||||||||| ||||||||||||||||||| ||||||||||| ||||| |||||||| |||||| ||| |||| ||||| || || || |||||
gtccgcatttcttaaaaaaatatggtcttatccactgcaaattgagtgacatttagattgtacagaattttgttcattgggacctcttgttgacatattctttttgttgtttctcctggcttaaaatatactattctttctgttcctggctcaatactttaaaacacaatattgatccacttttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGTGGAAATTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 3
tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtg-attgttgtatatgaccttg-tgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| | | | | ||||| | ||| || || | ||| || | | | | | | | | | | | ||| || |||||||||||| ||||||||||||||||||| ||||||||||| ||||| || |||||| |||||| ||| |||| ||||| || || || |||||
-tcttgttgacatattcttgttgtt-tctcctgacttaatttataatgttctttctgttccagactcgtactttaaaacacagtatcaatccaatcttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGCGGAAACTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 2
tac-atagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgttgtatatgacc---ttgtg-atctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
|| | || | | ||||| || || | | ||| || | | ||||| || | | || ||| || | ||||| |||||| | ||||||||||| ||| |||||||||||||||| || || |||||| | ||||||||||||| || || || ||||| || |||||||| || || |||||
aacgacgagaatgttaccttgttttgcacctgattggtgcctctacctgtact----gctttgtatttcagaatttaataagaactacttgtgtatctgt-gtagAAATTTGAGGGAGATGTTCAAGATTGATGCAGCGGATTATATGGTTTCCATTTGTGGAAGTGACGCACTTAGGGAGCTATCTTCTCCTGGAAAGAGTGGA
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
tacatagtaaggaaccattgttacagccccctttttttcttctc-tcttttcctttcactttgcatgtgattgttgtatatgacc-ttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
|| || | | ||| || ||||||| | | | | || | | | ||| ||| ||| ||| | ||| | ||| ||||| |||| ||| |||||||||| ||||| ||||| ||||||||||||||||||||||| ||| || | || |||||||||||||||||||| || ||
------gttagaacttgtg--tactgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgttgtat--atgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| | | |||| || |||| || | | | ||| | || | || | | | | | | ||| || ||||| || ||| |||| ||||||||||| |||||||| |||||||||||||| ||||| |||||||||||||||||||||||||| ||||||||||||
--tgtcttgatttaccaaaatttatagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ34272 (Selaginella moellendorffii), 3'ss of exon 2
tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgt----tgtatatgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
|| | | || ||||| || | ||| | || ||| | | |||| | || || | | ||| | | |||||| | ||||| || ||||||||||| |||||| | || ||||||||||||||||||| | |||||||||||||| || || |||||
-------------------gtcctacttttccttagctcttccgatttcccatttggcatttcatcttttgacgctctgtacagttttttttgttgcatgtcagGCACCTTAGAGAGCTTTTCAAAATCGATGCTGCTGATTATATGCTCTCTCTTTGTGGAAACGATGCTCTTCGAGAACTTTCTTCTCCGGGCAAGAGTGGC
upper sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 2
tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgttgtatatgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| | | | || | | |||| | ||| | || | ||||| || || | |||| | || || | | ||| | | |||||| | ||||| || ||||||||||| |||||| | || ||||||||||||||||||| | |||||||||||||| || || |||||
-----------gtcctacttttccttagctctttcgat-ttcccatttggcatttcatcttt--tgacgct-ctgtacagttttttttgttgcatgtcagGCACCTTAGAGAGCTTTTCAAAATCGATGCTGCTGATTATATGCTCTCTCTTTGTGGAAACGATGCTCTTCGAGAACTTTCTTCTCCGGGCAAGAGTGGCMapped 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|208106375|gb|GD906444.1|GD906444EST: CATCAATCAGAGGGTTTTAAATGGAA-GATTACTGCCCTATGGTATTCAG AAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTA
genomic: CATCAATCAGAGGGTTTTAAATGGAAAGATTACTGCCCTATGGTATTCAGgtaagtattg ... tctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttcctttcactttgcatgtgattgttgtatatgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
ttgtatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgttgtatatgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
- - - - - - - - - - - - - ccccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttgtg