Sequence
atgc intronic sequence ATGC exonic sequencegtgtgtatctagctttgctttttgattgaatcttgaattgttgcatatttgatgattgtgagcatgtttgcctttgtaattgaaatataattcttggtgttaaacgcagGTTGGGTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTTTGGGACCTTGGGGGACAGAGGAGGTTCCGGTCAATGTGGGAGCGATACT
Basic information
species | Glycine max |
transcript | GLYMA14G39540.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G171060_T02 (Zea mays), 3'ss of exon 4
gtgtgtatctagctttgctttttgattgaatcttgaattgttgcatatttgatgattgtgagcatgtttgcctttgtaattgaaatataattcttggtgttaaacgcagGTTGGGTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTTTGGGACCTTGGGGGACAGAGGAGGTTCCGGTCAATGTGGGAGCGATACT
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gtatgtacatacatacactttct--------------ttatggtgtccttaacaa------aaatctttgttatc-taagtgatctgaaatgcccatctgcgaa-acagGTAGGCTTCAATATGCGGAAAGTCACCAAGGGAAATGTCACGATTAAGCTTTGGGATCTTGGTGGGCAGCGGAGATTCCGCACTATGTGGGAGCGCTATT
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0006g01090.t01 (Vitis vinifera), 3'ss of exon 4
gtgtgtatctagctttgctttttgattgaatcttgaattgttgcatatttgatgattgtgagcatgtttgcctttgtaattgaaatataattcttggtgttaa-acgcagGTTGGGTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTTTGGGACCTTGGGGGACAGAGGAGGTTCCGGTCAATGTGGGAGCGATACT
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gtaggtatctttatccggggttaaattgaatttcacattgt----------atgatccttag--ttcttagatatcttatcaggg----attcttggctctgacaaacagGTGGGTTTCAATATGCGAAAAGTTACAAAGGGAAATGTAATAATAAAGGTTTGGGACCTGGGAGGGCAACAGAGGTTTCGTACCATGTGGGAGCGTTACT
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ07633 (Selaginella moellendorffii), 3'ss of exon 3
gtgtgtatctagctttgctttttgattgaatcttgaattgttgcatatttgatgattgtgagcatgtttgcctttgtaattgaaatataattcttggtgttaaacgcagGTTGGGTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTTTGGGACCTTGGGGGACAGAGGAGGTTCCGGTCAATGTGGGAGCGATACT
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------------------------------------gtaggaattctctcgatcgatccatccttgtct-cctccatgcctgacctgaggatctctctct----cgcagGTGGGATTCAACATGAGAAAAGTGACCAAAGGCAATGTGACGATCAAGCTGTGGGATCTGGGCGGACAACCACGCTTCCGGAGTATGTGGGAGCGCTATT
upper sequence: GLYMA14G39540.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ11035 (Selaginella moellendorffii), 3'ss of exon 3
gtgtgtatctagctttgctttttgattgaatcttgaattgttgcatatttgatgattgtgagcatgtttgcctttgtaattgaaatataattcttggtgttaaacgcagGTTGGGTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTTTGGGACCTTGGGGGACAGAGGAGGTTCCGGTCAATGTGGGAGCGATACT
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---------------------------------------gtaggaattctgtcgatcg-----atccatccttttctcctccatgcctgac-ctgaggatctctcgcagGTGGGATTCAACATGAGAAAAGTGACCAAAGGCAATGTGACGATCAAGCTGTGGGATCTGGGCGGACAACCACGCTTCCGGAGTATGTGGGAGCGCTATTMapped 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|208331608|gb|GE132321.1|GE132321EST: ACTGGGGGCTACAGTGAGGACATGATTCCAACT GTTGGTTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTT
genomic: ACTGGGGGCTACAGTGAGGACATGATTCCAACTgtgtgtatct ... ttaaacgcagGTTGGGTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgtgagcatgtttgcctttgtaattgaaatataattcttggtgttaaacgcagGTTGGGTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTTTGGGACCTTGGGGGACAGAGGAGGTTCCGGTCAATGTGGGAGCGATACT
tttgtaattgaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtatctagctttgctttttgattgaatcttgaattgttgcatatttgatgattgtgagcatgtttgcctttgtaattgaaatataattcttggtgttaaacgcagGTTGGGTTCAACATGAGAAAAGTGACTAAGGGAAATGTCACAATAAAGCTTTGGGACCTTGGGGGACAGAGGAGGTTCCGGTCAATGTGGGAGCGATACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG