Sequence
atgc intronic sequence ATGC exonic sequence...agattcagttttgaaaatttagcgttcaatcatcaattcctatgacttaatttggaaataacttatgaagttgctaagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
Basic information
species | Glycine max |
transcript | GLYMA04G07570.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G07570.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g15430.4 (Oryza sativa), 3'ss of exon 2
agattcagttttgaaaatttagcgttcaatcatcaattcctatgacttaatttggaaataactt--atgaagttgc-taagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
| | | ||| | || | | | | ||| | || ||||| ||| | ||| || || | || | | || || | | |||| | || | | | | ||||| | |||||||| || || |||||| |||||||||||||||| ||||| ||||||||||| || || ||
taagtaaatttgaagaaatgcgtgatgcgagatc---ttatagtacttagttttgtgctaaatttgatatggatgtattaactgaggtgattatacattacagGCCTAGCATATTGGCTTATCATTTCAAGACAGCTGTAGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCACAGCACT
upper sequence: GLYMA04G07570.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G116952_T03 (Zea mays), 3'ss of exon 2
agattcagttttgaaaatttagcgttcaatcatcaattcctatgacttaatttggaaataacttatgaagttgctaagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATT-CATCT----------------------------------
|||| | | | || | | ||||||| | | ||| || || || |||||| |||||||||||||||| ||||| ||||||||||| || | || |
------------------------------------------------------------------------------------------------acaggcttagtgtgctggcttatcacttcaagacaggtgttgactgtttctttgctgtatggtttgttgttggcaatgtgtggatttttggtgggcgcagTATTTCATCAGATGCTCAGGACGCTCCCAATATGTACAG
upper sequence: GLYMA04G07570.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G116952_T07 (Zea mays), 3'ss of exon 2
agattcagttttgaa-aatttagcgttc--aatcatcaattcctatgacttaatttggaaat---aacttatgaagttg-ctaagcttgcctgtacttgttta--acagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
| ||||| |||| || | || | || | || | | || || |||||| || | || | || | || || || || |||| | | | || | | ||||||| | | ||| || || || |||||| |||||||||||||||| ||||| ||||||||||| || | |
--------tcttgaagaattgagtggtctgatatattgagtcat-tagttttatctggaaactgaaatgaacattgtggtctgaactctgaagtgattacatattacagGCTTAGTGTGCTGGCTTATCACTTCAAGACAGGTGTTGACTGTTTCTTTGCTGTATGGTTTGTTGTTGGCAATGTGTGGATTTTTGGTGGGCGCAGTATT
upper sequence: GLYMA04G07570.2 (Glycine max), 3'ss of exon 2
lower sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------agattcagttttgaaaatttagcgttcaatcatcaatt----------cctatgacttaatttggaaataactt-------atgaagttgctaagcttgc-----ctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
| | |||||| |||| || ||| | || || | | | || ||| ||||| || || ||| || | || || ||| | |||| | || | | ||||||||||||||||| ||| | |||||||| ||||| | |||||||| || || ||||||||||| |||||||| |||||||||
gtaaacacacatgttcttagatgatctgtttcaactgaaagtttggattttgaattacgttttctctcaaagcttttcttatttttgagaattgagagtttagatgtctcttttgttctaaactttttctttgtgttgaaaatatctgcaatctaattgagtcagtatgattttggtcgttgattttggcttccagACTTAAAGTTATCGTGGAATACTTCAAAATGGCTCTGGATTGCTTCTTTGCGGTGTGGTTTGTGGTAGGTAATGTATGGATATTTGGAGGGCATTCATCT
upper sequence: GLYMA04G07570.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
agattcagttttgaaaatttagcgttcaatcatcaattcctatgacttaatttggaaata-acttatga-agttgctaagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
|| || || | | | | | | | ||| |||| || || | || | | || || | | | | | |||| | ||| | || |||||||||||||| || ||| | |||||||| |||||| | |||||||| || ||||| || ||||| |||||||| || || ||
--taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCAMapped 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|208115710|gb|GD908589.1|GD908589EST: AGTCGTGGTTGATGAATGCAAG ATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGC
genomic: AGTCGTGGTTGATGAATGCAAGgtactgagtt ... tgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGC
EST:
gi|207701551|gb|GD682880.1|GD682880EST: AGTCGTGGTTGATGAATGCAAG ATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGC
genomic: AGTCGTGGTTGATGAATGCAAGgtactgagtt ... tgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGC
EST:
gi|192303661|gb|FG995983.1|FG995983EST: GCATCTTCCAGAACTAGAAGCAATCAAGAGTCGTGGTTGATGAATGCAAG ATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGC
genomic: GCATCTTCCAGAACTAGAAGCAATCAAGAGTCGTGGTTGATGAATGCAAGgtactgagtt ... tgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttaatttggaaataacttatgaagttgctaagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
aaataac putative branch site (score: 2)
cttgttt putative PPT
aaataacttatgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agattcagttttgaaaatttagcgttcaatcatcaattcctatgacttaatttggaaataacttatgaagttgctaagcttgcctgtacttgtttaacagATTGAAGCTACTTGTGGAATACTTCAAAATTGCTGTAGATTGCTTTTTTGCTATATGGTTTGTTGTTGGAAATGTATGGATTTTTGGAGGACATTCATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - cctatga
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgcta