Sequence
atgc intronic sequence ATGC exonic sequencegtttttatacttccttttcccaaaataacttgttttccagtcatctacctatgaatataaacatcactaacatatatttgcagACTTTACATCGAATGTATATCATCAATGCTGGTCCTGGATTTAAGAGGATGCTTTGGCCTGCAGCACAGAAGTTTCTTGATGCCAAAACTATTGCAAAGA
Basic information
species | Glycine max |
transcript | GLYMA16G17830.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 7
gtttttatacttccttttcccaaaa-taacttgttttccagtcatctacctatgaatataaacatcactaacatatatttgcagACTTTACATCGAATGTATATCATCAATGCTGGTCCTGGATTTAAGAGGATGCTTTGGCCTGCAGCACAGAAGTTTCTTGATGCCAAAACTATTGCAAAGA
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gtacttgactttctcaattttacatctcatatgttcttcacatgcattcccagttgtttgaa-gtcatcatattat-tttgcagACGTTGCACAGAATGTACATTGTAAATGCTGGAACAGGTTTCAAAAAGATGCTTTGGCCTGCTGCTCAGAAGTTTCTTGATGCAAAGACCATTGCAAAGA
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 6
---------gtttttatact--tccttttcccaaaataacttgttttccagt------catctac-ctatgaata-taaacatcacta-----acatatatttgcagACTTTACATCGAATGTATATCATCAATGCTGGTCCTGGATTTAAGAGGATGCTTTGGCCTGCAGCACAGAAGTTTCTTGATGCCAAAACTATTGCAAAGA
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gtgccttctcttttcatgttatttcttttactgttgta-tttgtttttaattgttcaccatctctactaaaaataataattattattattgtcacatgcatttacagACACTACATCGAATGTTTGTTGTCAATGCCGGTCCTGGTTTCAAGAAGATGCTTTGGCCTGCTGCACAAAAGTTCCTTGATCCAAAGACAATATCAAAGA
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ17479 (Selaginella moellendorffii), 3'ss of exon 4
gtttttatacttccttttcccaaaataacttgttt-tccagtcatctacctatgaatataaacatcactaacatatatttgcagACTTTACATCGAATGTATATCATCAATGCTGGTCCTGGATTTAAGAGGATGCTTTGGCCTGCAGCACAGAAGTTTCTTGATGCCAAAACTATTGCAAAGA---
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-----------------------gtgagcctgctcgttgaactctatgcctttcttcctgagt-ttatgcgtttat-tatgcagACATTGCATCGTATGTTTATTATAAATGCTGGTCCTGGATTTAAGCTTGTG---TGGAACACCATACGGGGATTTTTAGATCCGAAAACAGCTACCAAAATAT
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28804 (Selaginella moellendorffii), 3'ss of exon 4
gtttttatacttccttttcccaaaataacttgttt-tccagtcatctacctatgaatataaacatcactaacatatatttgcagACTTTACATCGAATGTATATCATCAATGCTGGTCCTGGATTTAAGAGGATGCTTTGGCCTGCAGCACAGAAGTTTCTTGATGCCAAAACTATTGCAAAGA---
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-----------------------gtcagcctgctcgttgaactctatgcttttcttcctgagt-ttatgcgtttat-tatgcagACATTGCATCGTATGTTTATTATAAATGCTGGTCCTGGATTTAAGCTTGTG---TGGAACACCATACGGGGATTTTTAGATCCGAAAACAGCTACCAAAATAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgttttccagtcatctacctatgaatataaacatcactaacatatatttgcagACTTTACATCGAATGTATATCATCAATGCTGGTCCTGGATTTAAGAGGATGCTTTGGCCTGCAGCACAGAAGTTTCTTGATGCCAAAACTATTGCAAAGA
cactaac putative branch site (score: 1)
tatgaatataaacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttatacttccttttcccaaaataacttgttttccagtcatctacctatgaatataaacatcactaacatatatttgcagACTTTACATCGAATGTATATCATCAATGCTGGTCCTGGATTTAAGAGGATGCTTTGGCCTGCAGCACAGAAGTTTCTTGATGCCAAAACTATTGCAAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG