Sequence
atgc intronic sequence ATGC exonic sequencegttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
Basic information
species | Glycine max |
transcript | GLYMA01G40130.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 5
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgca--tgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctct----atccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
| || | | | | | | || || | || | ||| | |||| ||| || | ||| | | || |||| || || || |||| | ||| || || || ||||| ||||| | ||||| |||||||| ||||||||||| |||||||| || | || |||||||||||||| ||||| |
------------------------------------------------------------------------------------taaactaacataaaatttattaatgtggaaaatcaagaatttcctagtttgtttcata--acttactcttgactgttctttgtacttctgcttggcattcagGGAGTGCTCCTCTTACTGCTGTCCAACTGCTCTGGGTTAACATGATCATGGACACACTAGGAGCACTGGCATTGGCAACTGAACCTCCAAACGATGAACT
upper sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
||| | || | | | | || || | | || | ||| | | | || || | | | ||| || | ||||||| | || ||||| ||||| || || || |||||||||||||||| |||||||| |||||||| || || || || || || ||||| || || || |
---------------------------------------------------------------------------------------gtaagcttcca-aagaactggtgaaagcaatctgtcgccatgcatgcttgct--tgatctgctgctgctgctgcttgtgttgtgg--atccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
upper sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
| | ||| | | || | | || | || || |||| || | || | ||||||||| || ||| ||||| ||| || | || ||||||||| | ||||||||||||||||| ||||||||||| ||||| |||||| | ||||| || || ||||| || || |
----------------------------------------------------------------------------gtaggtttagtaagaataccaattcaatgtctcgaaaagaatca--ttttggattccttgtttgacacagctcttatgata--------atcttc-------agGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
upper sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
lower sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
||| || ||| | || || |||||| | | | | ||| || | | || | | | | || |||| ||| ||| ||| || | || || ||| |||||| ||| || || || ||||||||||| | ||||| |||||||| ||||||||||| ||||| |||||||| ||||| |||||||| || | || |
---------------------------------------------------gtaagt--taaagaaattagctgattctgtttttattcaaattttcat------ttttttacaattatattgtcttcgtttctatct--tta-----cttttgtttctaaattaatt-------cacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
upper sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 4
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
| ||| | | | || | || || || | | | || | ||| | |||| || | |||||| | || | || | |||| || | | | || | | ||||| ||| |||||||| |||||||| || ||||||| |||||||| ||||| ||||||||||| ||||| | || || || || || | |||||| ||
----------------------------------------------------------gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgt-caaataaacttcttcttttttctccctac-attttttttat--tccttttttttttcaaacacttaagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACCGAGCCACCTACTGATGACTT
upper sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 5
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
| ||| | | | || | || || || | | | || | ||| | |||| || | |||||| | || | || | |||| || | | | || | | |||||| ||| |||||||| |||||||| || ||||||| |||||||| ||||| ||||||||||| ||||| | || ||||| || || | |||||| ||
----------------------------------------------------------gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgt-caaataaacttcttcttttttctccctac-attttttttat--tccttttttttttcaaacacttcagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACTGAGCCACCTACTGATGACTT
upper sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 7
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttt-tgttttcacaccagcctgcatgacagattataaata-----aaaacactttttttgttttcttcttattagttatc-ttatgatcttacatgtattt------tctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
|||| || | ||| ||| | | |||| | | |||||| || ||| || ||| | ||| | | | | || || || ||||||||||| | | | | ||||| ||||| || || || || ||||| ||||||||||| ||| |||| |||||||| || || ||||||||| | |||||||| ||||| || || || |
---------------------------------------------------gtaaattttcagta-ttgcgcttctcggtttttttgaattaa---aggagacagaccatgtataccaatgaaccacctagtttaagagatcccagtgatttttcattgtgatcttacatacttgtacgacgttttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCTMapped 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|16279562|gb|BI943500.1|BI943500EST: CGTTAATGTGGTTGCATTAATAGTGAATTTCACATCAGCCTGCTTGACAG GAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
genomic: CGTTAATGTGGTTGCATTAATAGTGAATTTCACATCAGCCTGCTTGACAGgttagaaagt ... ctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
atcttac putative branch site (score: 3)
tattttctctatcc putative PPT
ttattagttatcttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA