Sequence
atgc intronic sequence ATGC exonic sequence...gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
Basic information
species | Glycine max |
transcript | GLYMA16G19350.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g24650.1 (Oryza sativa), 3'ss of exon 5
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
| || || | |||||| | |||| || | | || || || | | | || | | ||||||||||||||| ||| | || || |||||||||||||| ||| | ||||||||||| || ||||| || |||| |||||||| ||||| |||
------gtacttcccttttcagttac--ttgtgtga-gcaagcactggtttacttgttatggtgtatctacta--------ataatttccctgatcacagGTTCATTTTATTTCTGCTGCATGCGAAAATATGATAAGTGGCACAGGCATGAGGCCTGGTGACATTGTGACTGCTTCTAATGGAAAAACTATTGAG
upper sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G30920.1 (Arabidopsis thaliana), 3'ss of exon 5
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
| ||||| || | |||| ||| || || || | | || |||| || | ||||| | | | |||| |||| || |||||||| ||| | |||||||||||||||||||| || | ||||| ||||||||| | ||||| | ||||| |||||||| || |||
----gtaagttta----tcacacggagcttgcgt------ttctgagttaaatgaatg-tacctaaacaaatgcttcgttgcacaatc----------agGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACTGGAATGAGACCTGGAGATGTCCTCACAGCCTCAAACGGAAAGACGATTGAG
upper sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G24200.3 (Arabidopsis thaliana), 3'ss of exon 6
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
|| |||| || || ||||| | | || | | || | |||| | | || |||||| || | || ||||||||||| || |||||| ||||||| |||||||| |||||||| | ||||| ||||||||| | |||| | ||||| |||||||| || |||
----gttagttt----ctcccatc-agattcttt--tgaaagctatagtttgttaac---------cgaactgaacagattc---gtcttccacaaccagGTTCATTTCATCGTTGCAGCCTGTGAAAATATGATTAGTGGAACCGGAATGAGACCTGGAGATGTCATCACTGCCTCAAACGGAAAGACCATTGAG
upper sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G30910.1 (Arabidopsis thaliana), 3'ss of exon 5
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
| ||||| || | |||| ||| || || || | | | |||| || | ||||| | || |||| || |||||||| ||| | |||||||||||||||||||| || | ||||| ||||||||| | ||||| | ||||| || ||||| || |||
----gtaagttta----tcacacggagcttgagt------ttctgagttaagtgaatgtacctgaaca-aatgctt----------ctttgcacaattagGTGCACTTTATTGTCGCAGCTTGTGAGAATATGATAAGTGGTACCGGAATGAGACCTGGAGATGTCATCACAGCCTCAAACGGGAAGACAATTGAG
upper sequence: GLYMA16G19350.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0037g00180.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------gctaatttgtttag-agttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
||||| || | | | | || | || | | | || | | ||| | || | | | ||||| || | || ||||||| ||||| ||||||||| | |||||||||||||||||||||||| | |||||||||||||| |||||||| |||||||||||||||| || |||
gtaagccagttgttgttgttgttgttatcattgtttgtttgttttaacttgcatggaacaatttcttaactaatccatttgtatgttctattttcaattctccagca-attgaatctagcatacacttatgacttattaagggtcttgtatttgcagGTGCATTTCATTGTTGCAGCTTGTGAGAATATGATAAGTGGAACAGGCATGAGGCCTGGAGACGTTGTCACAGCTTCAAATGGAAAGACAATTGAGMapped 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|10234037|gb|BE802925.1|BE802925EST: ACGAAAGCTCTTGGTCAAATCAAAACTCTAGGGGTGGAG GTTCATTTTATTGTTGCAGCCTGTGAGAATATGATAAGTGGAACAAGTATG
genomic: ACGAAAGCTCTTGGTCAAATCAAACCTCTAGGGGTGGAGgtcagtcatt ... acatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
tattaat putative branch site (score: 2)
tattaatgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gctaatttgtttagagttctgatggagattgtgtagtgtcttttgtggtgtattaatgataatgcatgcaatgcccagattaaaaatcctacatgtgcagGTTCATTTTATTGTTGCAACCTGTGAGAATATGATAAGTGGAACAAGTATGAGGCCTGGAGATATTGTCACAACTTCAAATGGAAAGACTATAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - gatggag
- - - - - - - - - - - - - - - -tgtagtg
- - - - - - - - - - - - - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attaaaaa