Sequence
atgc intronic sequence ATGC exonic sequence...ccgcaattagaagcttagacactagtttatttataatgcaaatttttatgttttgtgtttgtatgctttggtgtgatgcctttctgcttgaatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG
Basic information
species | Glycine max |
transcript | GLYMA05G34420.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G076885_T01 (Zea mays), 3'ss of exon 1
ccgcaattagaagcttagacactagtttatttataatgcaaatttttat-gttttgtgtttgtatgct-ttggtgtgatgcctttctgcttgaatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG
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atgccttttactactgagatgacttttttactgtaaccgatttgcttgttgattcccctttccccactgtcaatttagtggctatttgtt--gattcggcagGTGTTAAGGATGGTTGTCAGCACATACCAAGCAGCAAGTGGTGCGGGTGCTGCGGCAATGGAAGAACTCAAGCTGCAGACTCAGGAG
upper sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G14810.1 (Arabidopsis thaliana), 3'ss of exon 1
-------ccgcaattagaagcttagacactagtttatttataatgcaaatttttatgtt--ttgtgtttgtatgctttggtg---tgatgcctttctgcttgaatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG
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gttcgatttttattctgaaatctgcttagtccaaaattttgaagggtagttagagaatcaatggaagctttagactttagtgctctgaataatgtttgattggctataatagGTGAAGAGAATGGTGGTTAGTACATATCAAGCAGCTAGTGGTGCTGGTGCTGCAGCTATGGAAGAGCTTGTTCAGCAGACTCGTGAG
upper sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0011g05860.t01 (Vitis vinifera), 3'ss of exon 1
ccgcaattagaagcttagacactagtttatttataatgcaaatttttatgttttgtgtttgtatgctttggtgtgatgcct--ttctgcttgaatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG
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gccaggccagttgcccaagtgtcttggggtttacttgggccatcatgtagttttg--gctgaacgctttacgatcgtgcttcattgtatgtgaatgttttagGTAGTACGCATGGTTGTCAGCACATATCAGGCAGCTAGTGGTGCTGGTGCTGCTGCAATGGAGGAGCTTGAACTGCAAACTCGTGAG
upper sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ30707 (Selaginella moellendorffii), 3'ss of exon 4
ccgcaattagaagcttagacactagtttatttataatgcaaatttttatgttttgtgtttgtatgctttggtgtgatgcctttctgcttgaatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG-------------
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--------------------------------gtgatttaagaatgtgttcctgctgcttccaagctttagtaaca----------ctggatgtttgtagGTAAAGCGCATGGTCGTGAGCACTTACCAAGCTGCGAGTGGAGCTGGTGCCGCTGCCATGGCGGAGCTTGAGCAGCAAACGCGTGAGGTCCTGGAAGGAA
upper sequence: GLYMA05G34420.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ28753 (Selaginella moellendorffii), 3'ss of exon 4
ccgcaattagaagcttagacactagtttatttataatgcaaatttttatgttttgtgtttgtatgctttggtgtgatgcctttctgcttgaatatt-gcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG-------------
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--------------------------------gtgatttaagaatgtgttgctgctgcttccaagctttagta------------actgggatgtttgtagGTAAAGCGCATGGTCGTGAGCACTTACCAAGCTGCGAGTGGAGCTGGTGCCGCTGCCATGGCGGAGCTTGAGCAGCAAACGCGTGAGGTCCTGGAAGGAAMapped 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|7796755|gb|AW782149.1|AW782149EST: CCACCATTATATGCTTGATGGCTGCTACCCCTCTTCATCGACGTGCCAAG GTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCT
genomic: CCACCATTATATGCTTGATGGCTGCTACCCCTCTTCATCGACGTGCCAAGgtccaacatt ... aatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCT
EST:
gi|254327091|gb|GR836700.1|GR836700EST: CCACCATTATATGCTTGATGGCTGCTACCCCTCTTCATCGACGTGCCAAG GTGTTACGTATGGTTGTTAGTACCTATCACGCTGCGAGTGGTGCTGGTGCT
genomic: CCACCATTATATGCTTGATGGCTGCTACCCCTCTTCATCGACGTGCCAAGgtccaacatt ... aatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgttttgtgtttgtatgctttggtgtgatgcctttctgcttgaatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG
ttgaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccgcaattagaagcttagacactagtttatttataatgcaaatttttatgttttgtgtttgtatgctttggtgtgatgcctttctgcttgaatattgcagGTGTTACGTATGGTTGTTAGTACCTATCAGGCTGCGAGTGGTGCTGGTGCTGCTGCAATGGAAGAGCTTGAGCTGCAAACTCGTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg