Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttctgtttatttgcttcagatatttatttaatttggtgttcttgttgggctatctgatttggtttctttctgaaaatcatgtcctagtttttcgtgtctgatggtcaatatgatctatcgcatgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCTGATCAGATAAGGGAATTGAGGGAAT
Basic information
species | Glycine max |
transcript | GLYMA14G07750.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0001g13090.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------gtaagtttttctgtttatttgcttcaga-----tatttatttaatttggtgtt--cttgttgggctatctgatttggtttctttctgaaaatcatgtcctagtttttcgtg--tctgatggtcaa-tatgatctatcgcatgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCTGATCAGATAAGGGAATTGAGGGAAT
| | ||| | || | ||| | ||| | ||||||| | | || || | | || || | || |||| | ||| ||| ||| || | | | || | | | || | ||||||||||||| ||||| || ||| | || || |||||||||||| |||| ||||| ||||| ||||| ||||| ||||| || | ||| | |||||||
gtaagttaccatggttctctatgtggactttgctgtgtaataccaactggataacttagtggcattagaattgatgattactccatttggtcatgattattttcaacattttagttagtgacaatcataaaagaaaaaagagagtttgtgtggttctcctgatagactgtgctatgatgatgtttaatagGTTGATCCAGTTGTTTATAACATGTTGCACGAAGATCCTGGTAATGTCAGCTACTCAGCTGTGGGTGGGTTATCAGATCAAATCCGAGAACTCAGGGAAT
upper sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S13_419V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaagtttttctgtttatttgcttcagatatttatttaatttggtgttcttgttgggctatctgatttggtttctttctgaaaatcatgtcctagtttttcgtgtctgatggtcaatatgatctatcgcatgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCTGATCAGATAAGGGAATTGAGGGAAT
| || |||| | || | || ||| | | || | | | | || | || |||||||| | || | | | | || | || | |||||||||| ||||| ||||| |||||||| ||||| ||||||||||| || ||||| |||||||| || || ||| || || | ||| | | || |
-----------------------ttaggatcttatatgtttgtgagtcgttggtaaaatttccaaata---tcttctccg-----------ctgatttttcgt-tttgtgcatttgtgcgcttgatt-cgtgcggttagGTTGATCCCGTAGTGTACAACATGCTTCACGAGGACCCTGGTAATATTAGCTACTCAGCTGTTGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGT
upper sequence: GLYMA14G07750.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S47_46V6.2 (Physcomitrella patens), 3'ss of exon 3
gtaagtttttctgtttatttgcttcagatatttatttaatttggtgttcttgttgggctatctgatttggtttctttctgaaaatcatgtcctagtttttcgtgtctgatggtcaatatgatctatcgcatgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCTGATCAGATAAGGGAATTGAGGGAAT
| |||| | | ||||| | | || | ||||| |||| || || | | | | | | | || | || ||||||| || ||||| ||||| |||||||||||||| || || |||||||| || || |||||||| || || ||| || || | ||| | | || |
-----------------------ttgcgaatttgtgatgtagaagacgcttgtcattgttccgcatccgttttct------aaattat-----agatgtaccgacttaacgcctgtcacaat-----gtgtgcgattagGTTGACCCCGTAGTGTACAACATGCTTCATGAGGACCCCGGAAATATCAGCTATTCAGCTGTTGGAGGACTAAGTGACCAAATTCGAGAACTTCGTGAGTMapped 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|24205449|gb|BU964702.1|BU964702EST: TGGTTCTTGATATGACCACGCTAACCATAATGCGAGCTCTTCCACGTGAA GTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGT
genomic: TGGTTCTTGATATGACCACGCTAACCATAATGCGAGCTCTTCCACGTGAAgtaagttttt ... atgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGT
EST:
gi|15813624|gb|BI785899.1|BI785899EST: TGGTTCTTGATATGACCACGCTAACCATAATGCGAGCTCTTCCACGTGAA GTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGT
genomic: TGGTTCTTGATATGACCACGCTAACCATAATGCGAGCTCTTCCACGTGAAgtaagttttt ... atgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatgtcctagtttttcgtgtctgatggtcaatatgatctatcgcatgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCTGATCAGATAAGGGAATTGAGGGAAT
gtctgat putative branch site (score: 4)
tagttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttctgtttatttgcttcagatatttatttaatttggtgttcttgttgggctatctgatttggtttctttctgaaaatcatgtcctagtttttcgtgtctgatggtcaatatgatctatcgcatgttgacagGTTGATCCAGTAGTTTACAATATGCTTCATGAGGATCCTGGTAATATCAGTTACTCTGCTGTTGGTGGTTTATCTGATCAGATAAGGGAATTGAGGGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG