Sequence
atgc intronic sequence ATGC exonic sequence...tgctttagattgttgttagttagtctctagttctctaccttgttcacttttctgctttatcactgatattgctattgcacatacgttttatgcattgcagGCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGGAAAGCAGTCGGCCGCCTGCAATCCCACAGCTTAACAGTGACACAGATGG
Basic information
species | Glycine max |
transcript | GLYMA20G25600.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G25600.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g38570.1 (Oryza sativa), 3'ss of exon 8
--------------------------------------------------------------------tgctttagattgttgttagttagtctctagtt-ctctaccttgttcacttttctgctttatcactgatattgctattgcacatacgttttatg----cattgcagGCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGGAAAGCAGTCGGCCGCCTGCAATCCCACAGCTTAACAGTGACACAGATGG
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gtaatgtatatctctggagtctggatatccatgaaatattttatcacatcttgtctggaaataacacatttctcaatttgtcctcatgtatggcatagtaacattagttcatgcacttta-tgctcgtagtttggcttgacgagtgtgatgtagtaatgtgaccttgttgcagGCTCAATCAGCACCAGTTGCTGAGATCTGGCTGTGGGAGGTTGGAACATGGAAAGCTGTTGGCCGCCTGCAATCTCACAACCTGACAGTTACACAGATGG
upper sequence: GLYMA20G25600.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G042371_T01 (Zea mays), 3'ss of exon 5
tgctttagattgttg--ttagttagtctctagttctctaccttgttcacttttctgctttatcactgatattgctattgcacatacgtttta-tgcattgcagGCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGGAAAGCAGTCGGCCGCCTGCAATCCCACAGCTTAACAGTGACACAGATGG
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---ttgacataattacatcagttgatgctggatatgcttaattattaatggtttgattttactgtatgcatgggaaatatgatggaatttcactcccattcagGCTCAATCAGCAGCAGTTGCAGAGATCTGGCTCTGGGAGGTTGGAACATGGAAAGCTGTTGCCCGCTTGCAATCTCACAGTCTAACAGTGACACAAATGG
upper sequence: GLYMA20G25600.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0011g04130.t01 (Vitis vinifera), 3'ss of exon 8
tgctttagattgttgttagttagtctc-tagttctctaccttgttcacttttctgctttatcactgatattg--ctattgcacatacgttttatgcattgcagGCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGGAAAGCAGTCGGCCGCCTGCAATCCCACAGCTTAACAGTGACACAGATGG
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---gatgtatagctgtatgtagaacttgcatttttttaccctgtgtttttgataggcatagaagttgttgcaaattattgctcatagattgcatattttgcagGCTCAATCAGCGAAAGTTGCAGAAATATGGCTATGGCAAGTGGGTTCATGGAAGGCAGTTGGTCGCTTGCAATCTCACAGCTTAACAGTGACACAGATTGMapped 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|193551627|gb|FK508510.1|FK508510EST: TTTCTTTATGTTGTGATCATAAGGGTGAGCTTGTTGCTTCTTCATGTAAG GCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGG
genomic: TTTCTTTATGTTGTGATCATAAGGGTGAGCTTGTTGCTTCTTCATGTAAGgtgagtggtg ... tgcattgcagGCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttctgctttatcactgatattgctattgcacatacgttttatgcattgcagGCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGGAAAGCAGTCGGCCGCCTGCAATCCCACAGCTTAACAGTGACACAGATGG
cactgat putative branch site (score: 3)
ttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgctttagattgttgttagttagtctctagttctctaccttgttcacttttctgctttatcactgatattgctattgcacatacgttttatgcattgcagGCTCAATCTGCAGCAGTTGCAGAGGTATGGCTTTGGCAGGTGGGTTCATGGAAAGCAGTCGGCCGCCTGCAATCCCACAGCTTAACAGTGACACAGATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
tgcttta
- - - - - tgttgtt
- - - - - - - - - - - - - - - - ctctacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatac