Sequence
atgc intronic sequence ATGC exonic sequence...accatcatattcgaactttttctgctcaccaaaatttaaggatagaatgatgaacattggaaaattattttcagatataattcacacaattattttacagGTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCAATAGGAT
Basic information
species | Glycine max |
transcript | GLYMA16G21560.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G21560.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G700662_T01 (Zea mays), 3'ss of exon 7
---accatcatatt--cgaactttttctgctcaccaaaatttaaggatagaatgatgaa--cattggaaaattattttcagatataattcac---acaattatt-----ttacagGTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCAATAGGAT
| | ||| || || | | | | | | || |||| | | | ||| |||| | | | || | | | ||||| | |||||| || | ||||||||| ||||| | ||||| |||| || || |||||||| |||||||||||||||||| | |||||||||| || || ||
gtgatcttcacatgggcggagggagtatcttttagggactccaatagaagaaggcttatatcatataggaattgtggttgtttctatcttatttgatgtttattcaaactaacagGTCGATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCTTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT
upper sequence: GLYMA16G21560.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G314386_T01 (Zea mays), 3'ss of exon 4
--accatcatattcgaactttttctgctcaccaaaatttaaggatagaatgatgaacattggaaaattattttcagatataattcacacaattattttacagGTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCAATAGGAT
| | | | ||||| | | |||| | | | | | | ||| ||| || | | || | || | | | | |||||| | || | ||||||||| ||||| | ||||| ||| || || |||||||| |||||||||||||||||| | |||||||||| || || ||
caatgaaaacttatatcttttttagggactccaatagaagaaggcatatacagtaaccgtggttgtttctatcttaat-tgatgtttatt-taaactaacagGTCTATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCCTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT
upper sequence: GLYMA16G21560.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G386125_T01 (Zea mays), 3'ss of exon 8
accatcatattcgaactttttctgctcaccaaaatttaaggatagaatgatgaacattggaaaattattttcagatataattcacacaa---ttatt-----ttacagGTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCAATAGGAT
|||| || | || | || ||| ||| | | | || | ||| |||| | | | || | | | ||||| | |||| | || | ||||||||| ||||| | ||||| |||| || || |||||||| |||||||||||||||||| | |||||||||| || || ||
----gcatagg-gagtatcttttagggactccaatagaagaa--ggcttat-atcatataggaattgtggttgtttctatcttatttgatgtttattcaaactaacagTTAGATCAGTGGATGGTGATAGCCAAGGCTTAGAGCGACTCTTTGGAGCTCTTTCTGCACATATGTGGCCTGGAATGATTCTGAAATCTGGAAACAGAAT
upper sequence: GLYMA16G21560.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0031g02260.t01 (Vitis vinifera), 3'ss of exon 4
accatcatattcgaactttttctgctcaccaaaatttaaggatagaatgatgaacattggaaaattattttcagatata-attcacacaa-----ttatt--ttacagGTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCAATAGGAT
||| | | |||| | ||| || || | ||| || |||| ||||| | || ||| | | || | || | ||||||||||| || ||||||||| |||||||||||| | || ||||||||||||||||||||||||||||||||| |||||||||| ||| |||
-------ccttcaacactattct-cccacaaagtttaggtcttggaaagagttccatttttcttcctttttcggtcatccatttatataaactggctgttcatgacagGTTTGTCAGTTAATGGTGATTCACAAGGAGTTGATAGAATCCTGGGTGCACTTTCTGCTCATATGTGGCCTGGAATGACCCTGAAATCTGGTGATAAGATMapped 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|192333176|gb|FK026505.1|FK026505EST: CAATATTGAGTTCATTGAG-CATGTGCTTCCAATGCTGATTTTGACAA-T GTTTGTCGATTGATGGTGATTT
genomic: CAATATTGAGTTCATTGAGGCATGTGCTTCCAATGCTGATTTTGACAAATgtaaaacttc ... tattttacagGTTTGTCGATTGATGGTGATTT
EST:
gi|151405714|gb|EV275528.1|EV275528EST: CAATATTGAGTTCATTGAGGCATGTGCTTCCAATGCTGATTTTGACAAAT GTTTGTCGATTGATGGTGATTTAC
genomic: CAATATTGAGTTCATTGAGGCATGTGCTTCCAATGCTGATTTTGACAAATgtaaaacttc ... tattttacagGTTTGTCGATTGATGGTGATTTAC
EST:
gi|151409293|gb|EV279101.1|EV279101EST: CAATATTGAGTTCATTGAGGCATGTGCTTCCAATGCTGATTTTGACAAAT GTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCAC
genomic: CAATATTGAGTTCATTGAGGCATGTGCTTCCAATGCTGATTTTGACAAATgtaaaacttc ... tattttacagGTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgatgaacattggaaaattattttcagatataattcacacaattattttacagGTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCAATAGGAT
ttatttt CT-rich tract
aaaattattttcagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accatcatattcgaactttttctgctcaccaaaatttaaggatagaatgatgaacattggaaaattattttcagatataattcacacaattattttacagGTTTGTCGATTGATGGTGATTTACAAGGAGTTGAGCGTCTCTACGGTGCACTTTCTGCTCATATGTGGCCTGGAATGGTATTGAAATCTGGCAATAGGAT
-ccatcat
- - - - - - - - - -ttctgct
- - - - - - - - - - - - - caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacacaa