Sequence
atgc intronic sequence ATGC exonic sequence...tttcctggtagaatgcaaattctcattctccgatccttttcagatctctttctgatttaaaattaactctagcatgacaattttcttttctttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATACGTAAAACAGCTTCCGCAGTATCCAAAACAAAACTTTT
Basic information
species | Glycine max |
transcript | GLYMA16G03670.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 4
tttcctggtagaatgcaaattctcattctccgatccttttcagatctctttctg-atttaaaattaactctagcatgacaattttcttttctttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATACGTAAAACAGCTTCCGCAGTATCCAAAACAAAACTTTT
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-ttttgggtccatttttttttctgttttctttgcttttctaaaatgtatccctgtaacccaagtggtatcaatattaatcagacccttttctcttcaaaagCTGATAGGGTCGCCAGATGACTCAAGCCTAGGGTTTCTTCGGAGTGATAATGCAAGAAGATACATGAAACAGCTACCACAGTACCCAAGGCAGGACTTCC
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 4
---tttcctggtagaatgcaaattctcattctccgatcctt--ttcagatctctttctgatttaaa-attaactctagcatgacaattttcttttctttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATACGTAAAACAGCTTCCGCAGTATCCAAAACAAAACTTTT
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ttaacttctattaatctgcaccattgagtacctttctcctttgttaaaatgctactataatctgggcattaatttta-----atgagttttttctcttccaaaa-gCTCATAGGCTCTCCAGATGATGCAAGCCTGGGATTTCTTCGAAGTGATAATGCAAAAAGATACATGAAACAACTACCACAGTTTCCAAGACAGGACTTCC
upper sequence: GLYMA16G03670.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 4
------tttcctggtagaatgcaaattctcattctccgatccttttcagatctctttctgatttaaaattaactctagcatgacaattttcttttctttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATACGTAAAACAGCTTCCGCAGTATCCAAAACAAAACTTTT
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agaactggtggtggcattgttggaaggtgaagtttctgtttctctt---atagcatt-tggttcaattctgatacttgctttgt--ttttctttttccttgaaaagCTTATAGGTTCACCTGATGACTCTAGCCTTGGGTTTCTTCGAAGTGATAATGCCCGAAGATATGTTAGGCAGCTACCACAATACCCGAGACAACAATTTCMapped 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|254331840|gb|GR846150.1|GR846150EST: CGCTCTTTCCTGGCAAAGATTATGTTCATCAGCTGAGACTTATCACAGAG CTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAAT
genomic: CGCTCTTTCCTGGCAAAGATTATGTTCATCAGCTGAGACTTATCACAGAGgtattagctt ... tttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAAT
EST:
gi|17519494|gb|BM188536.1|BM188536EST: CGCTCTTTCCTGGCAAATATTATGTTCATCAGCTGAGACTTATCACAGAG CTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAAT
genomic: CGCTCTTTCCTGGCAAAGATTATGTTCATCAGCTGAGACTTATCACAGAGgtattagctt ... tttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctttctgatttaaaattaactctagcatgacaattttcttttctttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATACGTAAAACAGCTTCCGCAGTATCCAAAACAAAACTTTT
aattaac putative branch site (score: 2)
caattttcttttcttt putative PPT
aattttcttttctttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcctggtagaatgcaaattctcattctccgatccttttcagatctctttctgatttaaaattaactctagcatgacaattttcttttctttcaaaaagCTGATAGGTTCGCCAGATGATGCCAGCCTTGGATTTCTACGAAGTGATAATGCTCGTAGATACGTAAAACAGCTTCCGCAGTATCCAAAACAAAACTTTT
tttcctg
- - - - - gaatgca
- - - - - - - - - - - -cattctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgac