Sequence
atgc intronic sequence ATGC exonic sequence...tttgtcttgataatgtgtataggtcagatttgtttgagatgttgatctatatttgagtactgaatgaaatgggtgttgtgttgatcattggtttgtgcagATTGTACATGATGAACTTGTACGATTGATGGGTGGAGAAGTTTCTGAACTGGTTTTTGCCAAATCTGGGCCCACTGTCATTTTATTGGCTGGACTTCAGG
Basic information
species | Glycine max |
transcript | GLYMA19G38110.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G38110.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g05552.1 (Oryza sativa), 3'ss of exon 4
-tttgtcttgataatgtgtataggtcagatttgtttgagatgttgatctat--atttgagtactgaatgaaatgggtgttgtgttgatcattggtttgtgcagATTGTACATGATGAACTTGTACGATTGATGGGTGGAGAAGTTTCTGAACTGGTTTTTGCCAAATCTGGGCCCACTGTCATTTTATTGGCTGGACTTCAGG
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gttattaattgtagtttgtgctagatgaacatggtgactatcttcttagactaatttatgtgct---tttagcacaggacaaataacctactcggtggtgcagATTGTGCATGATGAACTTGTAAAACTGATGGGTGGAGAAGTATCAGATCTGGTATTTGCAAAAAGTGGCCCCACAGTAATCTTACTGGCAGGCCTGCAAG
upper sequence: GLYMA19G38110.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G03940.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------tttgtcttgataatgtgtataggtcagatttgtttgagatgttgatctatatttgagtactgaatgaaatgggtgttgtgttgatcattggtttgt-gcagATTGTACATGATGAACTTGTACGATTGATGGGTGGAGAAGTTTCTGAACTGGTTTTTGCCAAATCTGGGCCCACTGTCATTTTATTGGCTGGACTTCAGG
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gtaattagcaataaaaccggttcttgtttttgtttcattagcataatggtttgatatttgattcactctatgatgatcattttggta-tcaatagtactcaagtgtggcttatcatggctttattgcagATTGTACATGATGAGCTAGTGAAATTGATGGGTGGAGAAGTATCTGAGTTACAGTTTGCTAAATCAGGTCCTACAGTAATATTGTTGGCTGGGCTCCAAG
upper sequence: GLYMA19G38110.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g03160.t01 (Vitis vinifera), 3'ss of exon 4
-----tttgtcttgataatgtgtataggtcagatttgtttgagatgttgatctatatttgagtactgaatgaaatgggtgttgtgttgatcattggtttgtgcagATTGTACATGATGAACTTGTACGATTGATGGGTGGAGAAGTTTCTGAACTGGTTTTTGCCAAATCTGGGCCCACTGTCATTTTATTGGCTGGACTTCAGG
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caatcccagcttccaaccaatatgaaaggcaaaaacgtatag--tcttggttttcactt--atagttcctggaattatgaatatat-ggttcttggttagtgcagATTGTACATGATGAGCTTGTGAAATTGATGGGTGGAGAGGTATCTGAACTGGTTTTTGCAAAATCTGGCCCCACTGTGATATTATTGGCTGGTCTACAAGMapped 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|193606398|gb|FK555639.1|FK555639EST: TGGGTGTTGGTGTCATTCGAGGAGTGAGACCGGATCAGCAATTGGTTAAG ATTGTACATGATGAACTTGTACGATTGATGGGTGGAGAAGTTTCTGAACTG
genomic: TGGGTGTTGGTGTCATTCGAGGAGTGAGACCGGATCAGCAATTGGTTAAGgtaaaatcat ... gtttgtgcagATTGTACATGATGAACTTGTACGATTGATGGGTGGAGAAGTTTCTGAACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctatatttgagtactgaatgaaatgggtgttgtgttgatcattggtttgtgcagATTGTACATGATGAACTTGTACGATTGATGGGTGGAGAAGTTTCTGAACTGGTTTTTGCCAAATCTGGGCCCACTGTCATTTTATTGGCTGGACTTCAGG
tgttgat putative branch site (score: 4)
aatgaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtcttgataatgtgtataggtcagatttgtttgagatgttgatctatatttgagtactgaatgaaatgggtgttgtgttgatcattggtttgtgcagATTGTACATGATGAACTTGTACGATTGATGGGTGGAGAAGTTTCTGAACTGGTTTTTGCCAAATCTGGGCCCACTGTCATTTTATTGGCTGGACTTCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- tgtcttg
- - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - -gatgttg
- - - - - - - - - - - - - - - - - - - -tgttgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgtt