Sequence
atgc intronic sequence ATGC exonic sequencegttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
Basic information
species | Glycine max |
transcript | GLYMA12G27300.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
| | | | ||||||| | | || | ||| | || || |||| || ||| ||||| || || || ||||||||||||||||| | || || ||||| ||||| ||||||||||| || || || | || ||| | ||||| |||||||| |||||||| ||||| |
----------------------------------------------gtagctgtgcgtttttctttaaacagtttgctgctt-actgaactt---tttaccc---aag---------tctgtgtcctg---atgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
upper sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 5
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
| || ||| | ||| | | ||| | | || | | | | | || |||||||||||||||||| | || || ||||| ||||| ||||| ||||| || || || || || ||| ||||||| |||||||| |||||||||||||| |
--------------------------------------------------------------------gtact-tgtgcatttgctaaataaatttattagtagtgagcttttatagacaaggctgtttcaatgcagGCAGATATCTGGTCTTTAGGTATCACTGCCATTGAAATGGCTAAAGGTGAACCCCCTCTGGCAGATATTCATCCCATGAGAGTTCTTTTCATCATACCTC
upper sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 9
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttt-tatcccctaagaatcatcac----tctgtatcttgt-ttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
|| ||| | | | || || | | ||| || | | | | | || | | | ||||||| || ||| | ||| | | |||| ||| || || | ||||||||||| |||||||| || || || ||| |||||||||||||| || ||||| |||||||| |||||||| |||||||||||||| ||||| ||||
---------------gtatctcgtccatctgctgtagcttttgttgttcttctagtttacccaatctt-ctgtgtataccctggctttacttgttttctagccctttctaattttgtcggtttctgcttctggtcttttccagGCAGATATATGGTCTCTTGGAATAACAATGATAGAGATGGCAAAAGGAGAACCTCCCCTTGCTGACCTTCATCCTATGAGAGTGCTTTTTATCATTCCCC
upper sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G15220.1 (Arabidopsis thaliana), 3'ss of exon 9
gttatcttatagttactactcaaat-catttattat-gctttctgagttcatcctaacatatt-tcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
||||| || |||| | | || || | | |||| || | | | | | || |||| | | || | ||||| || | | || | | |||| || |||||||||| ||||| || || || || | ||||||||||||||||| || ||||| || ||||| |||||||| |||||||||||||| ||||| || |
-gtatctcgcctata-tactgagcttcacttctcctagcttgacatgtgtgtttgtagaggctatacttgtttccttagcatatctaatattttttgccttcttttt------ctgttgctgggattgttgtc-atttagGCAGATATTTGGTCGCTCGGAATAACAGTTATTGAGATGGCAAAAGGAGAACCTCCCCTAGCTGACCTTCATCCCATGAGAGTGCTTTTTATCATTCCTC
upper sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 9
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
| | | || | || | | | ||| || ||| | ||| | ||| || || | | || | | | || | | | || ||||| ||||| ||||||||||| || ||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||||||||||| || ||||| |
-------------------------------tgaggtggtcagtatttgtgttt-ctccttttttgccatgttttgtccatttggtgcttcc---tcccacttctgata-ttattgggccatgaacaatg-atgcagGCGGATATTTGGTCTCTGGGAATAACTGCAATTGAGATGGCAAAAGGGGAGCCTCCACTTGCAGATCTCCATCCAATGAGAGTGCTTTTTATAATACCTC
upper sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S84_190V6.1 (Physcomitrella patens), 3'ss of exon 7
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCC---TCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
| ||| | | || ||| | || | | | | | | | || ||||| | | |||||| | | | || ||| | || || | ||||||||||| || || |||| || ||||| |||||||||||||||||||| | | | | ||| ||
-----------ttcacttccc--gtcgtttgtgttgaagaggatgatggtagtgataaaaagctattcatt-tgtattccttcaatat---------------ctgagagcaagtggcttgcat--------tgcagGCAGATATATGTTCATTGGGAATCACTGCTATTGAGATGGCAAAAGGGGAACTGTATTCTCCAAGAGATTTT-------------------------------
upper sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
| || ||| ||| | | | | | | | ||| | || || || | | ||| | | || | ||||||||||| ||||| |||| || || || ||||||||||||||||||||||| || || ||||| ||||| ||| | || ||||| | || ||
----------------------------atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcattctcattcattcaatagc-tgagagcaggtgattttcat--------tgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTAMapped 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|207838828|gb|GD810476.1|GD810476EST: TTTGGATGGCACCCGAGGTTATTCAAAATTCAGAAGGATATAATGAGAAG GCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAG
genomic: TTTGGATGGCACCCGAGGTTATTCAAAATTCAGAAGGATATAATGAGAAGgttatcttat ... gtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
tcttgttt CT-rich tract
tttttgtttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT