Sequence
atgc intronic sequence ATGC exonic sequence...agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
Basic information
species | Glycine max |
transcript | GLYMA10G06800.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
--agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| | || || | ||| | ||| | | | | || || |||| || | || | || | | | | | | ||| ||||||||||| ||| ||||||||||||||||||| || |||||||| || || ||||||||| ||| || ||||| | ||||||||||| || |||||
taccttttttcttttctttttattcttatttctagcttatagttctcttctttctgtcacac-acctaaaatggccat-tgttcttattttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------agtaaggaactactgtt-acatccccctttt----ttccttctctctt------tttcattcctttcacttt--acatgtgattgttatatatgaccttg-tgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| ||| || |||| |||| | |||| || || || ||| | |||| || | | | | | | | | | ||| | || ||| || |||||||||||| ||||||||||||||||||| ||||||||||| ||||| ||||||||| |||||| ||| |||| ||||| || || || |||||
gtccgcatttcttaaaaaaatatggtcttatccactgcaaattgagtgacatttagattgtacagaattttgttcattgggacctcttgttgacatattctttttgttgtttctcctggcttaaaatatactattctttctgttcctggctcaatactttaaaacacaatattgatccacttttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGTGGAAATTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 3
agtaaggaactactgttacatcccccttttttcctt---ctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacc----tgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| || | || | || |||| || ||| | || || || || | | || | || | | | | ||| || |||||||||||| ||||||||||||||||||| ||||||||||| ||||| || ||||| |||||| ||| |||| ||||| || || || |||||
-------tcttgttgacatattcttgttgtttctcctgacttaatttataatgttctttctgttccagactcgtactttaaaacacagtatcaatccaatcttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGCGGAAACTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G076392_T02 (Zea mays), 3'ss of exon 2
agtaaggaactactgttacatcccccttttttccttctctct----ttttcattcctttcactttacatgtgattgttatatatgacc---ttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
||| || | | || | |||| | || | | | | |||| || | | || ||| || | ||||| || ||||||||||| ||| |||||||||||||||| || || |||||| | ||||||||||||| ||| || || ||||| || |||||||| || || |||||
-------aacgacgagaatgttaccttgttttgcacctgattggtgcctctacctgtactgctttgtatttcagaatttaataagaactacttgtgtatctgtgtagAAATTTGAGGGAGATGTTCAAGATTGATGCAGCGGATTATATGGTTTCCATTTGTGGAAGTGACGCACTTAGGGAGCTATCTTCTCCTGGAAAGAGTGGA
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
|| || |||| ||| || | |||||||| | | | || | | | | | || | |||||| ||| | ||| ||||| |||| ||| |||||||||| ||||| ||||| ||||||||||||||||||||||||||| || | || |||||||||||||||||||| || ||
-gttag-aacttgtgt-actgcatacttttttcttagtagtatgttaactatagtagttgtgtccttggtgtttatattca---ttgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0007g04700.t01 (Vitis vinifera), 3'ss of exon 2
agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatat--atgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
|| || ||| | || || || | | || | ||| | ||| | || | | | | | | || ||| || ||||| || ||| |||| ||||||||||| |||||||| |||||||||||||| |||||||||||||||||||||||||||||||| ||||||||||||
tgtcttgatttacca--aaatttatagaattaaattttgttaattaatgtacttaagatgcacacctttctgaaaactcaagtgcttgattactgattgaagGAATTTAAGGGAGATGTTTAAGATTGATGCCGCTGACTACATGATGTCCATTTGCGGAAATGATGCTCTGAGGGAACTTTCTTCTCCTGGGAAAAGTGGT
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ34272 (Selaginella moellendorffii), 3'ss of exon 2
agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacctg--ttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| || || ||| | |||| | || || | | | | | | || || | || | ||| | | |||||| | ||||| || ||||||||||| |||||| | || |||||||||| |||||||| | |||||||||||||| || || |||||
-----------------gtcctacttttccttagctcttccgatttcccatttggcatttcatcttttgacgctctgtacagttttttttgttgcatgtcagGCACCTTAGAGAGCTTTTCAAAATCGATGCTGCTGATTATATGCTCTCTCTTTGTGGAAACGATGCTCTTCGAGAACTTTCTTCTCCGGGCAAGAGTGGC
upper sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ31327 (Selaginella moellendorffii), 3'ss of exon 2
agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacctg--ttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
| || || ||| || |||| | || || | | | | | | || || | || | ||| | | |||||| | ||||| || ||||||||||| |||||| | || |||||||||| |||||||| | |||||||||||||| || || |||||
-----------------gtcctacttttccttagctctttcgatttcccatttggcatttcatcttttgacgctctgtacagttttttttgttgcatgtcagGCACCTTAGAGAGCTTTTCAAAATCGATGCTGCTGATTATATGCTCTCTCTTTGTGGAAACGATGCTCTTCGAGAACTTTCTTCTCCGGGCAAGAGTGGCMapped 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|19934888|gb|BQ079927.1|BQ079927EST: CATCAATCAGAGGGTTTTAAATGGAAAGATTACTGCCCTATGGTATTCAG AAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCAT
genomic: CATCAATCAGAGGGTTTTAAATGGAAAGATTACTGCCCTATGGTGTTCAGgtaagtattg ... cctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcattcctttcactttacatgtgattgttatatatgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
tgattgttatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT
- - - - actactg
- - - - - - - - - -atccccc
- - - - - - - - - - - - - - - - ccttctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttgtg