Sequence
atgc intronic sequence ATGC exonic sequence...gtgtccatttttagtagccgacggtgtttcaaacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
Basic information
species | Glycine max |
transcript | GLYMA09G40690.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g60190.1 (Oryza sativa), 3'ss of exon 2
-gtgtccatttttagt--agccgacggtgtttcaaacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttaca-gGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
| ||||| || || | | | ||| | | |||| | | | || ||| | | | | || ||||| | ||| | |||||| || || |||||||||| || | ||||||||| || ||||| || ||||| | |||||||||||||| || || ||||| |||||||||||||
tgattccatgttgtgttgggttgcccttgtgctatgaatttacgcctttgcct----gcactctagtttcagcagttaactctattttttttgtacattaaaagGGTGCTCCCGAGAGGTGGAGATTAGTGAAGGCTCATGGAACAGCTGTTGGTCTTCCTAGCGAAGATGACATGGGCAACAGCGAAGTGGGTCACAATGCTC
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G833389_T02 (Zea mays), 3'ss of exon 2
gtgtccatttttagtagccgacggtgtttca--aacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggatttttat-tgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
|| | | | ||| | |||| | || || | | | | | || | | | ||| | | | || ||| | |||| || ||||| |||||| | || | ||||||||| || ||||| ||||| ||| | || ||||||||||| || |||||||||||||||||||| |
---tctttctcttgtaagaaagattgttctgtcagcataatttgttttgcaggtatactgtctatatgcttttacttacccttcagtgaaatatgtatattagGGCGCTCCTGAGAAATGGAGACTAGTGAAGGCTCATGGAACAGCTGTGGGCCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCAC
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G003385_T02 (Zea mays), 3'ss of exon 2
gtgtccatttttagtagccgacggtgtttcaaacagggttgc---ctccgaaccg-aagtagactggttagatgaaattaatcaggatttttat-tgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
| || | | | | | | ||| | || | || | | ||| |||| | ||| | | | | | || | | ||||||| ||||| |||||| | || | ||||||||| || ||||| || || ||| | || ||||||||||| || |||||||||||||||||||| |
-----ctttctcacggacgaaagattgttctgttctgtcagcataatttgatttgcaggtatactgtcttcatgcactcacccttttgtgaaatacatgtattagGGTGCTCCTGAGAAATGGAGACTAGTGAAGGCTCATGGAACAGCTGTGGGTCTCCCATCTGATGATGACATGGGCAACAGTGAAGTTGGTCACAATGCAC
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G08590.2 (Arabidopsis thaliana), 3'ss of exon 1
----gtgtccatttttagtagccgacggtgtttcaaacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggat--ttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
|| ||| ||||| | | | || | | | | | | | | | ||| || | || | | | ||||||| | | |||||| || || ||||| ||| | | |||||||||||||| || || || || | ||||| |||||||| || ||||||||||| ||||||||||
gtatgtttccttttttgtttatatccacttctttcctcgatgatttcgctggatt--------ccgatta--tggacttcaacggttcgattttattct-tcacagGGGAAGCCCGACACATGGAGGTTGATCAAAGCTCATGGTACCGCCGTTGGTCTCCCCAGCGAAGACGACATGGGAAACAGTGAAGTTGGCCACAATGCTC
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0056g00200.t01 (Vitis vinifera), 3'ss of exon 1
gtgtccattt-ttagtagccgacggtgtttcaaacagggttgcct--ccgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
| ||| ||| | | || || | | | || || | | || || || | ||| ||| | || | ||||||||||||||| ||||||||||||| ||||||||| | || ||||| |||||||| || ||||||||||| || ||||||||||| || |||||||
---ttcatgcattaaaggattattatgcttggtgcctgcctcacttacctcattattgaaggctcaataatgtctgtcaattgttttttattttccttcacagGGTGCCCCTGAGAAATGGAGATTGGTTAAGGCTCATGGGAGTGCAGTAGGGCTTCCAACTGAGGATGACATGGGCAACAGTGAAGTTGGCCATAATGCTC
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ14459 (Selaginella moellendorffii), 3'ss of exon 1
gtgtccatttttagtagccgacggtgtttcaaacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
| | | | | | | |||| | ||| | ||| | | || || |||| || |||||| || ||||||||| | || | ||| ||||| | || || ||||||||||| || ||||||||||| |||||||| |||||||||||||||
-------------------------------gtaaaagcgctttttggatctggat---ctggatcgat-----tgatcttgttgctttttttcttttagACTGCCCCCGATCGGTGGAGACTTGTCAAGGCGCATGGACCTGCCGTCGGCCTTCCAACCGAGGATGACATGGGAAATAGTGAGGTTGGTCACAATGCTT
upper sequence: GLYMA09G40690.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ26058 (Selaginella moellendorffii), 3'ss of exon 1
gtgtccatttttagtagccgacggtgtttcaaacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
| | | | | | | || | | ||| | ||| | | || || |||| || ||||| || ||||||||| | || | ||| ||||| | || || ||||||||||| || ||||||||||| |||||||| |||||||||||||||
-------------------------------gtaaaagcgctttttggatccggat---ctcgatcgat-----tgatcttgttgctttttttcttttagACCGCCCCCGATCGGTGGAGACTTGTCAAGGCGCATGGACCTGCCGTCGGCCTTCCAACCGAGGATGACATGGGAAATAGTGAGGTTGGTCACAATGCTTMapped 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|207784630|gb|GD756533.1|GD756533EST: ACAACTGCATCCACAAGGCTGAAACACCCTGCATGGATTCTCTTAAAAAG GGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGC
genomic: ACAACTGCATCCACAAGGCTGAAACACCCTGCATGGATTCTCTTAAAAAGgttcattttt ... tgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
aattaat putative branch site (score: 3)
tttttatt putative PPT
aaattaatcaggattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtccatttttagtagccgacggtgtttcaaacagggttgcctccgaaccgaagtagactggttagatgaaattaatcaggatttttattgtcttacagGGTGCCCCTGAACGGTGGAGATTGGTTAGGGCTCATGGTACCGCTGTAGGCCTTCCAACAGAAGATGACATGGGTAATAGTGAAGTTGGTCACAATGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - tcaaaca
- - - - - - - - - - - - - - - - - - - -tgcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - actggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaattaa