Sequence
atgc intronic sequence ATGC exonic sequencegtatgtgtaatgtttaacacttcttttactttatcttttggctcttttacttgttgaccccctaatctacttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
Basic information
species | Glycine max |
transcript | GLYMA04G01240.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 10
---------------------------------------------------------------gtatgtgtaatgtttaacacttcttttactttatcttttggctcttttacttgttgaccc-cctaatc-------tacttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
| | | | ||| | | || || ||| | | | | | | | || |||| |||| ||||| |||| |||| || || ||||| |||||||||||||| ||||| | || |||||||| | || ||||||||||||||||||||||| |||||
gtaagcaactcaataatttaaatttatttcattcaaaagcatggaacattcagatatgaaacagcactcctgagttttgtga--tgattcaccttacttatcaatggtgatgtctataaatccgtttaattatatgaatactatgtgcagGTTTTGAAGATTAACCCTTTGAAGAAGGATATAGATTCTTTCGTGGCATCAGACTTCAAGCTGGTCGGTTATGATCCTCACCAGAAGATTGAAATGAAAA
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G157586_T01 (Zea mays), 3'ss of exon 1
-----------gtatgtgtaatgttt-aacacttcttttactttatcttttg-gctcttttacttgttgaccccctaatctacttcttgca--gACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
|| | | ||||| | ||||||| |||| || || | | | | | | | | | | | |||| || |||| |||||||||| ||| || ||||||||||||||| |||| | || |||||||| | ||||||||||| ||||||||||| || |||||
gtgagccactcctaatagaactgttttgatgtttctttttgtttactttctgtgaccatgcatcttctaagttctatgtgggccttatgcacagATTTTGAAGATAAATCCTTCAAAAAAGGATATAGATTCTTTTATGGCATCAGACTTCAAGCTGGTTGGCTATGATCCCCACCAGAAGATAGAGATGAAAA
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G005990_T01 (Zea mays), 3'ss of exon 10
-----------gtatgtgtaatgttt-aacacttcttttactttatcttttg-gctcttttacttgttgaccccctaatctacttcttgca--gACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
|| | | ||||| | ||||||| |||| || || | | | | | | | | | | | |||| || |||| |||||||||| ||| || ||||||||||||||| |||| | || |||||||| | |||||||| || ||||||||||| || |||||
gtgagccactcctaatagaactgttttgatgtttctttttgtttactttctgtgaccatgcatcttctaagttctatgtgggccttatgcacagATTTTGAAGATAAATCCTTCAAAAAAGGATATAGATTCTTTTATGGCATCAGACTTCAAGCTGGTTGGCTATGACCCCCACCAGAAGATAGAGATGAAAA
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
lower sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 11
------------------------------------------gtatgtgtaatgtttaacacttcttttact--ttatcttttggctcttt-tacttgttgaccccctaatctacttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
|| || || || | || | | | ||| | || |||| || | | ||| || | | | || ||| |||| ||||||||||| | ||||||||||||||||||||||| || | ||| || ||||||| ||||||||||||||| |||| || ||||||||
gtgagtataaacaaacacatgatttgctgattcttcaatcttgtttgagtt-tgatgaatgcataatctaccaataattctttgcaactatatgcttatttatctttggga----tatttacagGTTTTGAAGATAAATCCAGAGAAGAAAGATATAGATTCTTTTGTTGCGGATGACTTTGAGCTCATTGGCTATGATCCTCACAAGAAAATAGATATGAAAA
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------gtatgtgtaatgtttaacacttcttttactttatcttttggctcttttacttgttgaccccctaatctacttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
||| | | || | | || || | ||| | |||| |||| | | | || | ||||| || ||||||| || | |||||| | || ||||||||||||||| |||| || | |||| |||||||||||||||| ||||||| || |||||
gtaagtatatcgccgacaatgatcatcgaggaatgcatattc-acctatccttaccgtgtttttgtttgtcg---tcatgggctcactactgcagGTAATGAAGATAAACCCGGAGAAGAAACAAATCGATTCTTTTGTGGCTTCTGACTTTGACCTCACAGGCTATGATCCTCACAAGAAGATAGAAATGAAAA
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0001g12940.t01 (Vitis vinifera), 3'ss of exon 9
------------gtatgtgtaatgtttaacacttcttttactttatcttttggctcttttacttgttgaccccctaatctac---------ttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
| | | | | | || || || || | ||| | ||| | ||| ||| | ||| | ||| |||||| |||| |||| |||||| | ||||| ||||| || || |||||||| |||||||| |||| ||||| ||| ||||||||||||||||||| |||||
caaggtagctctgcctttttcttatataccattttttaagtactttctcctagctactaccctttctgaacttctatgttgtctttgcctgttcctgcagATTTTGAAGATCAATCCACAGAAGAAGGATATTGAATCATTTGTGGCAGCTGATTTTGAGCTTATAGGTTATAATCCTCACCAGAAGATTGAAATGAAAA
upper sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 11
--------------------------------------------------------------gtatgtgtaatgtttaacacttcttttactttatcttttgg---ctcttttacttgttg-----accccctaatctacttctt---gcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
| | | ||||| |||| | || || | |||| || ||| | ||||| | || || | | || ||||| |||| |||| |||||| | ||||| | || |||||||||||||| ||||||||| | |||||||| ||||||||||| ||||| || || |||||
gttagtattcttgaattgattagttctattccaaattttttatttgtaaggagtataattcctttcttcttgtgtttttcactcttattctttcgtatttttctctctatttgagttgttccatacatcctcttactcgcactttaatgcagATTTTGAAGATCAATCCACAGAAGAAGAACATTGATTCTTTTGTGGCAGCTGATTTCCAACTCATAGGTTATGATCCTCATCAGAAAATAGAGATGAAAAMapped 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|208159540|gb|GD955289.1|GD955289EST: ATGTGAGGCCTTTGCAGGAGCAGCTCCATAACCAGCCAAAACCTTTTCCA ACTTTGGAGATAAATCCAAAAA-GAAAGATATAGATTCTTTTGTGGCTGCT
genomic: ATGTGAGGCCTTTGCAGGAGCAGCTCCATAACCAGCCAAAACCTTTTCCAgtatgtgtaa ... cttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCT
EST:
gi|20498259|gb|BQ273189.1|BQ273189EST: ATGTGAGGCCTTTGCAGGAGCAGCTCCATAACCAGCCAAAACCTTTTCCA ACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCT
genomic: ATGTGAGGCCTTTGCAGGAGCAGCTCCATAACCAGCCAAAACCTTTTCCAgtatgtgtaa ... cttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttactttatcttttggctcttttacttgttgaccccctaatctacttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
ccctaat putative branch site (score: 3)
tctacttctt CT-rich tract
tttatctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtgtaatgtttaacacttcttttactttatcttttggctcttttacttgttgaccccctaatctacttcttgcagACTTTGGAGATAAATCCAAAAAAGAAAGATATAGATTCTTTTGTGGCTGCTGATTTCAAGCTCATAGGCTATGATCCTCACCAGAAGATTGATATGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC