Sequence
atgc intronic sequence ATGC exonic sequencegttagccttttagccattccagttgtatctggaccatctgatgtttcctagttggttaagaattaattttctgacataagtaaaaccaattccttcttttgatgttattttaacttgtatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
Basic information
species | Glycine max |
transcript | GLYMA10G38820.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G38820.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G151580_T01 (Zea mays), 3'ss of exon 2
gttagccttttagccattccagttgtatctggaccatctgatgtttcctagttggttaagaattaattttctg-acataagtaaaaccaattccttcttttgatgttattttaacttgtatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
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--------------------------------------------------gatagtgccatatccattttctatatcttattttcgtagatt--ttcctttgattctatggta--ttgtcataggtcatattcatgaagttttgtttg--ccacagGATGATAAAAACATTGCTCATTTGACTCATGTGAGTGAGATGGAAAAGAAGTGCGAGTCTTTGGCCAGAATGACTGCAATTTTGAAAGATGTAATTCAGA
upper sequence: GLYMA10G38820.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G32980.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagccttttagccattccagttgtatctggaccatctgatgtttcctagttggttaagaattaattttctga--cataagtaaaaccaattccttcttttgatgttat---tttaacttgtatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
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-gtatctttctcatggttttggtttctttttcaaattgaaataagatatggatcatagtatttgcattgcctgaagccttatgataacttattggtatatctcatgtaacaacttttgttagatgctttgtatataacttcttttgttggcgaatttcagGATGATAAAAATGTGGCGCATTTGACTCATGTTGGTGAAATGCAAAAGAAAATCGAGACTTTGTCAAGGATTACTCAAATATTGAAAGATGTTATACAAA
upper sequence: GLYMA10G38820.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0059g01290.t01 (Vitis vinifera), 3'ss of exon 2
gttagccttttagccattccagttgtatctggaccatctgatgtttcctagttggttaagaattaattttctgacataagtaaaaccaattccttcttttgatgttattttaacttgtatctgtctactcatctagagatttg--taaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
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--------------------------------------------------------caaggat-aattttttggtctcttttacttgaatctgtttatttgaaaattttatactgggcacttcctaactgacatgtttgttgaattggattgtttagGAAGATAAGAATGTGGCACATCTCACGCATGTAAGTGAAATGGAAAAGAAGTGTGAGACTTTAGCAAGGATTACTGCTATATTGAAAGATGTTATTCAAAMapped 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|254320595|gb|GR827044.1|GR827044EST: CCGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAG GATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAG
genomic: CCGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAGgttagccttt ... aaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAG
EST:
gi|14011814|gb|BG726736.1|BG726736EST: CCGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAG GATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAG
genomic: CCGTCCAAAGAAAAATTGCAGATTTGCAAGTTGAACTTCAAGGTCGAAAGgttagccttt ... aaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgttattttaacttgtatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
ttttaac putative branch site (score: 2)
ttttt putative PPT
tagagatttgtaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagccttttagccattccagttgtatctggaccatctgatgtttcctagttggttaagaattaattttctgacataagtaaaaccaattccttcttttgatgttattttaacttgtatctgtctactcatctagagatttgtaaaatttttagGATGACAAAAATGTTGCACATTTGACTCATGTGAGTGAAATGGAAAAGAAGATTGAGACATTGGCAAGGATTACTACTATACTCAAAGATGTTATTCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG