Sequence
atgc intronic sequence ATGC exonic sequencegtacgtcttattcttcaatttcaaaaatggactgatgagtgttcacattaatggtttcatatgctttatacagcaatgacttacttctgtttgaagattgctttctatgaagcaatatgttcataactatgcttttaggtatgtttgaaaatatgaaatgtctcaaataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGG
Basic information
species | Glycine max |
transcript | GLYMA08G03340.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0016g02430.t01 (Vitis vinifera), 3'ss of exon 5
gtacgtcttattcttcaatttcaaaaatggactgatgagtgttcacattaatggtttcatatgctttatacagcaatgact-tacttctgtttgaagattgctttctatgaagcaatatgttcataactatgcttttaggtatgtttgaaaatatgaaatgtctcaaataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGG
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--------------------------------------------------------------------------aacctctgtgtgtctgtgcaaaggat--catgaaccatgtgcctttctcttgcttgt-ctctaaaggatgtgtgggatctaacttcggcccctggtttctcagGTTGGAGATTTTGGACTGGCAAGGTGGCAGCCAGATGGAGACATGGGAGTGGAAACACGAATAATTGGAACATTTGG
upper sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S336_36V6.1 (Physcomitrella patens), 3'ss of exon 6
gtacgtcttattcttcaatttcaaaaatggactgatgagtgttcacattaatggtttcatatgctttatacagcaatgacttacttctgtttgaaga-ttgctttctatgaagcaatatgttcataactatgcttttaggtatgtttgaaaatatgaaatgtctcaaataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGG
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----------------------------------------------------------gtatgcatcgta--gcagaaattcttttcaattcaagtagttccatttcctactcctaagctggcagattcttacacttgagtagtcattgagagaagttttgt-tctttggatatcagGTGGGAGATTTTGGACTCGCAAGATGGCAGCCAGACGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACTTTCGG
upper sequence: GLYMA08G03340.2 (Glycine max), 3'ss of exon 4
lower sequence: PP1S59_359V6.1 (Physcomitrella patens), 3'ss of exon 5
gtacgtcttattcttcaatttcaaaaatggactgatgagtgttcacattaatggtttcatatgctttatacagcaatgacttacttctgtttgaagattgctttctatgaagcaatatgttcataactatgcttttaggtatgtttgaaaatatgaaatgtctcaaataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGG
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--------------------------------------------gtatgtggcgttccacacactgtttcgaacggtaaat-gtttctgttt----attg---tctgaatggccacatgcctattcctaa---tgtggttac---cgacagcac-aagtgttttttg-gatatcagGTTGGAGATTTTGGACTTGCAAGATGGCAACCAGATGGACATTGTGGTGTGGAGACCAGGGTTATTGGCACCTTCGGMapped 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|26269266|gb|CA820329.1|CA820329EST: GTGACATGCGGCCTAACAATATTCTCCTCACTCATGATTTTGAAGCTTTA GTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTG
genomic: GTGACATGCGGCCTAACAATATTCTCCTCACTCATGATTTTGAAGCTTTAgtacgtctta ... ataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cataactatgcttttaggtatgtttgaaaatatgaaatgtctcaaataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGG
tcataac putative branch site (score: 2)
aaaatatgaaatgtct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgtcttattcttcaatttcaaaaatggactgatgagtgttcacattaatggtttcatatgctttatacagcaatgacttacttctgtttgaagattgctttctatgaagcaatatgttcataactatgcttttaggtatgtttgaaaatatgaaatgtctcaaataattttagGTAGGAGATTTTGGACTAGCAAGGTGGCAGCCAGATGGAGACATGGGTGTGGAAACCAGGGTCATAGGAACATTTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA