Sequence
atgc intronic sequence ATGC exonic sequence...ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtttcttgagcttgaggcatgtgcttacttattttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
Basic information
species | Glycine max |
transcript | GLYMA09G32740.1 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G070273_T01 (Zea mays), 3'ss of exon 20
ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtttcttgagcttgaggcatgt---gcttacttatt--ttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
|| ||||| | | | | | ||||| | || ||| ||| | | ||| |||| | | ||||| ||||||||||| ||||||||||| || || |||||||| |||||||| | || | || | || ||||| ||||| || || || || | || |
-----atatttctgctggaactaaagtccttgagctgttgcaattaatgtccaagtttgtttcatattaaagggaagaattgacagtgtttctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCAGGTTCAGCAGGAAAGCAATTGAAAGAAGCGCAAAGTATAAATAAATCTCTTTCTG
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G109420_T01 (Zea mays), 3'ss of exon 6
ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtt--tcttgagc--ttgaggcatgtgcttacttatt--ttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
| | ||| | | | | | | | | | | | | ||| || || | | ||| ||| |||| | | ||||| ||||||||||| ||||||||||| || || |||||||| || ||||| | || | || | || ||||| |||
-gtacgcgttgcg-cgccactgcacgccgaggcgaagctttcgccgatggcgatgactagctggcctatctacgtacgaattgacagTGTTTCTCTGTTTGAACAGCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCAGCAGGAAAGCAATTGAAAGAAGCGCAAG---------------------
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
lower sequence: GRMZM2G423861_T02 (Zea mays), 3'ss of exon 20
--ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtttcttgagcttgaggcatgtgcttacttatt--ttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
|||| | || | || ||| || | || | | |||| || | | | | | | | ||| |||| | | ||||| ||||||||||| ||||||||||| || || |||||||| || ||||| | || | || || || ||||| ||||| || ||||| || | || |
tgtgaaactattgcatc----ctaaacagtccttgggcttttgtagagtttgtttcacattacacttacggggaagaattgacagtgttcctctgtttgaacagCTAAGTTTTGTGGACCTTGCTGGTTCTGAGAGGGTGAAAAAATCTGGTTCCGCAGGAAAGCAACTGAAAGAAGCACAAAGTATAAACAAATCTCTTTCTG
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
lower sequence: AT5G65930.2 (Arabidopsis thaliana), 3'ss of exon 19
ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtttcttgagcttga-ggcatgtgcttacttatttta---tgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
| || || ||| || || || || | | | || | | ||| | || || || | || |||| | | ||| | || ||||||||||||||||||||||||||||||| || ||||| |||||||| || || |||| |||| || || ||||||||||| || ||||| ||| | || |
---atattattagtcaatgatatgccctccattgttaaacccat-atcacctgatcatggtggtatcttctacaatattctgaatttttgtttgttatttgcagCTGAGTTTTGTGGATCTTGCTGGTTCTGAGAGAGTTAAAAAGTCGGGCTCAGCTGGTTGTCAACTCAAAGAAGCTCAAAGTATCAACAAATCACTTTCTG
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 21
ggaaaatgtttcttcattgt---taagcaacaatatggaacatcaattgtt-tcttgagcttgaggcatgtgcttacttattttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
|| ||| | ||| | | || | | | | | || || | | | || | ||| |||| | | | | || || ||||||| ||||||||||||||||||||||||||||| ||||| || ||||| ||| | || | ||| |||||||||||||||||||| ||||||||| | ||||
--aatctgtgttaacatggagtgtgagatgtcttgttggggcttacttattgtgataatgttta--tttgtctttacatgacaattttaaaactctatctgcagCTAAGTTTTGTGGATCTTGCTGGTTCAGAAAGGGTGAAGAAATCAGGCTCTTCAGGTAATCAACTTAAGGAAGCTCAAAGCATCAACAAGTCACTTTCAG
upper sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 22
lower sequence: PP1S199_47V6.1 (Physcomitrella patens), 3'ss of exon 23
---ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtttcttgagcttgaggcatgtgcttacttattttatgttgga-ttcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
| | ||| ||| | ||| | ||| | || || | | || | | | || || || ||||||| ||||| ||| | |||||||||||||||||||||||| || || ||||||||||| || || || || | ||| || || || || || ||||||||||| || || || ||||
caagaatggtgtgccttgttagtttcgtcacattttgtaa--ttagcaattgcactatttcttgg--tgaatttctgaattttattttggacttctctgagcagCTGAGTTTTGTGGATCTTGCGGGCTCTGAAAGAGTGAAGAAATCTGGATCCAGTGGTGAACAACTGAAAGAGGCCCAAAGCATTAATAAATCTTTGTCAGMapped 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|13790109|gb|BG652700.1|BG652700EST: TTGTAATTGAAAGTACCAACCTTCAAAGTCAGTCAGTTGCAAGGGGAAAG CTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCT
genomic: TTGTAATTGAAAGTACCAACCTTCAAAGTCAGTCAGTTGCAAGGGGAAAGgtatatttta ... caatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttcttgagcttgaggcatgtgcttacttattttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
tgcttac putative branch site (score: 2)
ttacttattttatgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaaaatgtttcttcattgttaagcaacaatatggaacatcaattgtttcttgagcttgaggcatgtgcttacttattttatgttggattcaatatgcagCTGAGTTTTGTGGATCTTGCTGGTTCAGAAAGAGTGAAAAAGTCAGGTTCTACTGGGAGTCAGCTTAAGGAAGCTCAAAGCATTAACAAGTCATTATCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - -cttcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttgg