Sequence
atgc intronic sequence ATGC exonic sequenceggtctgatttatgtatccatttagtttgattcactttctagttgtgtttttgttttgcttgtgtttgcatggatgttgtttgatgtgttttgttttgggtttaGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTTCGTGTTGATAAGGTCCTCCAGCCC
Basic information
species | Glycine max |
transcript | GLYMA18G10430.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G10430.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G55120.1 (Arabidopsis thaliana), 3'ss of exon 3
ggtctgatttatgtatccatttagtttgattca-ctttctagttgtgtttttgttttgcttgtgtttgcatggatgttgtttgatgtgttttgttttgggtttaGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTTCGTGTTGATAAGGTCCTCCAGCCC-
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agtttcaggttcacattgttgatatttacttgagctgaagaatcaattttctgtttcacat-tgttg--atgtttggttgttggtgtgcattggt--aataatagGTTATACCGGGGAAGTACGGTTTCATTGCGCAGCTGAATGAAGGTCGGCATCTCAAGAAGAGACCAACCGAGTTCCGTGTTGACAAAGTTCTTCAACCAT
upper sequence: GLYMA18G10430.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G26850.1 (Arabidopsis thaliana), 3'ss of exon 3
----------ggtctgatttatgtatccatttagtttgattcactttctagttgtgtttttgttttgcttgtgttt-gcatggatgttgtttgatgtgttttgttttgggtt-taGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTTCGTGTTGATAAGGTCCTCCAGCCC-
| || | | | || ||||| || || | |||| | | ||||| ||| |||| || ||||| || ||| ||||| || || ||| ||||||||||| |||||||||| || |||||||||||| | |||||||| ||||||||||| ||||| |||||||| | ||| |
gtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacat---tgttcttaagattgtttctcttgatgttatagGTTATCCCGGGGAAGTATGGTTTCGTTGCTCAGCTTAACGAGGGTCGTCACTTGAAGAAGAGGCCAACTGAGTTCCGTGTAGATAAGGTGTTGCAGTCTT
upper sequence: GLYMA18G10430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv19s0090g01000.t01 (Vitis vinifera), 3'ss of exon 3
----ggtctgatttatgtatccatttagttt-------gattcactttctagttgtgtttttg--ttttgcttgtgtttgc-----------atggatgttgtttgatgtgttt--tgttttgggtttaGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTTCGTGTTGATAAGGTCCTCCAGCCC-
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gtcagatattgattctgttcatctttagtttctttcctagttcgttgacaaattgggttttgggtttttcattgtggctgccaactggggttgtgggtttctctcaatttgtttgttaattcctgaccagGTGATTCCGGGTGAGTATGGGTTCATTGCCCAGCTGAATGAGGGCCGCCACCTGAAGAAGAGGCCCACTGAGTTCCGTGTGGATAAAGTCCTCCAGCCCTMapped 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|27446264|gb|CA953387.1|CA953387EST: TGTGAAACCAA GGTGATTCCTGGGGAGTATGGTTTCATTGCTCATCTGAATGAGGGTCGTCA
genomic: TGTGAAACCAAggtctgattt ... tttgggtttaGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgttttgcttgtgtttgcatggatgttgtttgatgtgttttgttttgggtttaGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTTCGTGTTGATAAGGTCCTCCAGCCC
gtttgat putative branch site (score: 5)
ttttgtttt putative PPT
ttttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggtctgatttatgtatccatttagtttgattcactttctagttgtgtttttgttttgcttgtgtttgcatggatgttgtttgatgtgttttgttttgggtttaGGTGATTCCTGGGGAGTATGGTTTCATTGCTCAGCTGAATGAGGGTCGTCACCTCAAGAAGAGACCAACTGAGTTTCGTGTTGATAAGGTCCTCCAGCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA