Sequence
atgc intronic sequence ATGC exonic sequencegtattgcaatcttgtatgattattctctctccaggtgtgtgagaaccataatatgtaacttctatcttcggactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
Basic information
species | Glycine max |
transcript | GLYMA02G09390.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G008556_T01 (Zea mays), 3'ss of exon 5
-------------------------------------gtattgcaatcttgtatgattattctctctccaggtgtgtgag-aaccataatatgtaacttctatcttcggactttgccatcaacttcct---cagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
| || | | || ||| | ||| | | | || || | | | | ||| | || || | || | ||||||||||||||||| || ||||| ||||| | || ||| | ||||| ||||||||||| | ||||||||| ||||| | ||||||||||| ||| ||
gtaagtgggtgcatgcagtttattctctatcatgaaaacacaataacttggcattccaattgaatagtttagtgcctaattgattattat-tattattattattattat-tattattattattttgcattgcagGAAGAAAATAAAATCTTAGACAAGCTGCATCGCCAAAAGATTGCAGAAGTTGAAAAGCTGAGCCAAACTGTGAGAGAGTTGGAAGAGGCTGTTCTTCAAG
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G017525_T01 (Zea mays), 3'ss of exon 1
----------gtattgcaatcttgtatgattattctctctccaggtgtgtgagaaccataatatgtaacttctatcttcggactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
|| | || | | || | || | | | ||| | |||||| | | ||| | || |||| | | |||||||| || ||||| ||||| | |||||| | ||||| || || ||||||||||||||||| || ||||| ||||| |||||||| |||| ||||| |
gtacgcgacagtggagatattcattgacactagtaactttaccagcttgtttgc-ccataa---gctaacagtatatgagg-ctttcctgttgcaccaaacagGAAGAGAACAAAATCTTGGATAGAATGCACCGCCAGAAAGTTGCTGAGGTTGAAAAGCTCACGCAGACTGTCAGAGAGCTAGAAGAATCTGTTCTTGCTG
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G24764.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattgcaatcttgta-tgattattct-ctctccaggtgtgtgagaaccataatatgtaacttctatcttcggactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
| ||| | || | ||| | | | | || || | | | |||| | || || || | |||||||||| |||||| | || | ||||||||| |||||||| || || || |||||||| || || || || |||| |||||||||||||| |||||||
--------gttctgtggtcgccatcttgttctttgtatttacttaatctatgg-atttgccaacaatctgattaactt--tattttctgttttagGAAGAAAACAAAATTCTAGATAGAATGCATAGGCAGAAGGTTGCTGAAGTGGAAAAGCTTACTCAGACAGTACGAGAGCTAGAAGAGGCTGTTCTTGCAG
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G14840.2 (Arabidopsis thaliana), 3'ss of exon 5
----gtat-tgcaatcttgtatgattattctctctccag----gtgtgtgagaaccataatatgtaacttctatcttcggactttgccatcaacttcct----cagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
|| | | || | | | |||| | |||| | || | || | | ||| | | | || || | | | ||||||| |||| |||| | ||||| ||||| ||||||||||| ||||| ||||||||||| | || | |||| | ||| ||||||| ||||| ||||| |
gtatgtctatatcatttcttttacatattggaacaccagaatagggtatctcttccttttcttaccactgtggtggccttatttgttgatacattggttaaaatagGAAGAGAATAGAATTATAGACAAGATGCACAGACAGAAGGTTGCAGAAGTTGAAAAGCTTATGCAGAGTGTTCGGGAATTAGAAGAAGCTGTTCTTGCTG
upper sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------gtattgcaatcttgtatgat----tattctctctccaggtgtgtgagaaccataatatgtaacttctatcttcggactttgc-----------catcaacttcctc--------agGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
| | || | |||| || | || ||| | ||| | || | | ||||| | | | | || || |||| | | | |||||||||||||||||||||| || |||||| | || ||||| |||||||||||||| || ||||||||||| || || || ||||||||||| || || |
gtattgtgattgcccatgctgttttgttttccaatgcaatgtgaacttggggcatattatcttttcttttattttgttttggattttttttgtgtaatcttcctttgtttaattagcatgagtttatatgtcaaatccttttgtatactagGAAGAAAATAAAATTTTGGATAAGATGCATCGCCAAAAGGTTGCAGAGGTTGAAAAACTAACCCAAACTGTAAGGGAGCTTGAAGAGGCTGTTCTGGCTGMapped 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|254322365|gb|GR837779.1|GR837779EST: ACCTGCAGAACAAAAATCAAGAGCTAATTAAACAGATTGAGATTTGCCAG GAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAG-TGGCAGAGGTT
genomic: ACCTGCAGAACAAAAATCAAGAGCTAATTAAACAGATTGAGATTTGCCAGgtattgcaat ... acttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTT
EST:
gi|14990947|gb|BI316620.1|BI316620EST: ACCTGCAGAACAAAAATCAAGAGCTAATTAAACAGATTGAGATTTGCCAG GAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTT
genomic: ACCTGCAGAACAAAAATCAAGAGCTAATTAAACAGATTGAGATTTGCCAGgtattgcaat ... acttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgagaaccataatatgtaacttctatcttcggactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
atgtaac putative branch site (score: 3)
cttcctc putative PPT
ataatatgtaactt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgcaatcttgtatgattattctctctccaggtgtgtgagaaccataatatgtaacttctatcttcggactttgccatcaacttcctcagGAAGAAAATAAAATTTTGGACAAAATGCATAGACAGAAGGTGGCAGAGGTTGAAAAGCTCACCCAAACTGTTAGAGAACTAGAAGAGGCTGTCCTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG