Sequence
atgc intronic sequence ATGC exonic sequencegtatgcaagacatcctccttttatcattttgcattcagtaggacaaaaaattagattgtaatgtagccatgagtgaaagctttgaaaacatacatctggtttagttactgttgcaattgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
Basic information
species | Glycine max |
transcript | GLYMA01G01000.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G01000.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g53810.1 (Oryza sativa), 3'ss of exon 2
gtatgcaagacatcctccttttatcattttgcattcagtaggacaaaaaattagattgtaatgtagccatgagtgaaagctttgaaaacatacatctggtttagttactgttgcaattgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
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-----------------aagtcctcatttttcatcccacagga--gatgattagatt----tctagaaattttgtaaagccaaggcaaagctaataaggataaatt--tgcc-cgtttgtgaacagATATGTGATCATAGGGAACCATCGTGATGCCTGGACATTCGGAGCAGTTGATCCCAACAGTGGAACAGCAGCTATGCTCGAG
upper sequence: GLYMA01G01000.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G159171_T01 (Zea mays), 3'ss of exon 2
gtatgcaagacatcctccttttatcattttgcattcagtaggacaaaaaattagattgtaatgtagccatgagtgaaagctttgaaaacatacatctggtttagttactgttgcaattgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
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--------------aaatttgtcaaattttgccaacaatataattagatatcag--catcatgt---catgggca-----tctagaaacttga--caaatttaaatactgtttgacatatttgcagATATGTGATCATAGGCAACCATCGTGATGCTTGGACATTTGGAGCAGTTGATCCTAACAGTGGAACAGCAGCCATGCTTGAG
upper sequence: GLYMA01G01000.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G19740.1 (Arabidopsis thaliana), 3'ss of exon 2
gtatgcaagacatcctccttttatcattttgcattcagtaggacaaaaaattagattgtaatgtagccatgagtgaaagctttgaaaacatacatctggtttagttactgttgcaattgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
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-------------------------------------------gtacattttcaatagtga-gtggcaatagacttctgattgtagtaactaactagggattgtatatgaatg-gattggt--tagATATGTGATTCTTGGGAACCATAGAGACGCTTGGACTTTTGGAGCTGTTGATCCGAACAGTGGCACTGCGGTACTTATGGAG
upper sequence: GLYMA01G01000.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g03010.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------gtatgcaagacatcct------ccttttatcattttgcattcagtaggacaaaaaattagat-tgtaatgtagccatgagtgaaagctttgaaaacatacatctggttt---agttactg--ttgcaattgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
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gtatgttgaaaatcttccaaagtagtaatgcaggtattaagtaggaactgctgaaacaagtagggtgttttaatatgtattaaaccactaaacatccatagaagtggcacaaaagctctttaatagggaaattgatcgata-tgaaggacctcacctttaatttcatagtcactgaattgcaattcctt-tagATTTGTTCTTCTTGGTAACCACCGGGATGCCTGGACATTTGGAGCTGTTGATCCCAATAGCGGCACTGCAACTCTGCTTGAG
upper sequence: GLYMA01G01000.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ15056 (Selaginella moellendorffii), 3'ss of exon 2
gtatgcaagacatcctccttttatcattttgcattcagtaggacaaaaaattagattgtaatgtagccatgagtgaaagctttgaaaacatacatctggtttagttactgttgcaattgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
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------------------------------------------------------------------------gtaagtaatctaagacttcagattcttttggggcgctataattgaatgttcaagGTATATTTTGCTCGGAAACCATCGAGATGCATGGACATTTGGAGCAGCCGACCCCAACAGTGGCACTGCATGTCTTCTTGAA
upper sequence: GLYMA01G01000.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ37632 (Selaginella moellendorffii), 3'ss of exon 2
gtatgcaagacatcctccttttatcattttgcattcagtaggacaaaaaattagattgtaatgtagccatgagtgaaagctttgaaaacatacatctggtttagttactgttgcaattgcttgt---agATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
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------------------------------------------------------------------------gtaagtaatctaagacttcagattc--ttttgcgac-gctataattgaatgttcaagGTATATTTTGCTCGGAAACCATCGAGATGCATGGACATTTGGAGCAGCCGACCCCAACAGTGGCACTGCATGTCTTCTTGAAMapped 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|12773686|gb|BG238613.1|BG238613EST: ACAATTCAAAATGTTATTGGTGTGATTGAAGGGGCAGAAGAGCCTGACCG ATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGA
genomic: ACAATTCAAAATGTTATTGGTGTGATTGAAGGGGCAGAAGAGCCTGACCGgtatgcaaga ... ttgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtgaaagctttgaaaacatacatctggtttagttactgttgcaattgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
tttgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcaagacatcctccttttatcattttgcattcagtaggacaaaaaattagattgtaatgtagccatgagtgaaagctttgaaaacatacatctggtttagttactgttgcaattgcttgtagATTTGTCATACTAGGTAACCATAGGGATGCATGGACATTTGGAGCGGTTGATCCCAATAGTGGCACTGCAGCACTGCTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG