Sequence
atgc intronic sequence ATGC exonic sequence...tcattgatctaggtgctttcttaatattatgtatctggtggatgcatactgaatcgtattatcctgttgaatgttgatatattttagttactatttgcagTGCAAATGTTTTTGGAGTTTCAACAGAATCTATGCAGCTGTCTTTTGATGCCAGAGGAAATAGTGTTCCTACAATACTGCTGTTAATGCAAAGACATTTG
Basic information
species | Glycine max |
transcript | GLYMA03G35480.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g05900.1 (Oryza sativa), 3'ss of exon 1
---tcattgatctaggtgctttcttaatattatgtatc-tggtggatgcatactgaatcgtattatcctgttgaatgttgatatattttagttactatttgcagTGCAAATGTTTTTGGAGTTTCAACAGAATCTATGCAGCTGTCTTTTGATGCCAGAGGAAATAGTGTTCCTACAATACTGCTGTTAATGCAAAGACATTTG
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tttgcactgataatatggaattttgagcaatatcgattatgcttaatttttgtttgat----ttagcatccgagattgtgagctgattaaaactttacttgcagTGCAAGTGTCTTTGGAGTTTCAACAGAATCGATGCAGTGCTCCTATGATTCCAGAGGAAACAGTGTCCCAACAATTCTCTTGATGATGCAAAGACGTCTT
upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g05540.1 (Oryza sativa), 3'ss of exon 1
tcattgatctaggtgctttcttaatattatgtatctggtggatgcatactgaatcgtattatcctgttgaatgttgatatattttagttact---------atttgcagTGCAAATGTTTTTGGAGTTTCAACAGAATCTATGCAGCTGTCTTTTGATGCCAGAGGAAATAGTGTTCCTACAATACTGCTGTTAATGCAAAGACATTTG
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------atgacactgtacttttgataa-atatactctagaatttagttcttgttcatgtttac--accagctgttggtatttgtcagctgatcaaaacttaaaatgcagTGCAAGTGTCTTTGGCGTTTCAACAGAATCAATGCAATGTTCCTACGATTCCAGAGGAAACAGTGTACCAACGATTCTCTTGATGATGCAAAGACGTCTT
upper sequence: GLYMA03G35480.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g03140.t01 (Vitis vinifera), 3'ss of exon 1
-tcattgatc-taggtgctttcttaatattatgtatctggtggatgcatactgaatcgtattatcctgttgaatgttgatatattttagttactatttgcagTGCAAATGTTTTTGGAGTTTCAACAGAATCTATGCAGCTGTCTTTTGATGCCAGAGGAAATAGTGTTCCTACAATACTGCTGTTAATGCAAAGACATTTG
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gcttctgttcattaatgcatacttgttatcgtgt--ccgacatttttgtgcaagtgtttaggctaatgttgcattattgactttgatatccttcacctgcagTGCAAATGTTTTTGGAGTTTCCACAGAGTCTATGCAGCTTTCATTTGACTCTAGAGGGAACAGCGTGCCTACAATACTCCTGCTTATGCAAAGACGCTTGMapped 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|207816386|gb|GD787913.1|GD787913EST: TTGCCTGTGGAGTTCGAACCAGAAGTTCCCAGGAGACCTCCCAGAGCTAG TGCAAATGTTTTTGGAGTTTCAACAGAATCTATGCAGCTGTCTTTTGATGC
genomic: TTGCCTGTGGAGTTCGAACCAGAAGTTCCCAGGAGACCTCCCAGCGCTAGgtaacttggg ... ctatttgcagTGCAAATGTTTTTGGAGTTTCAACAGAATCTATGCAGCTGTCTTTTGATGC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atactgaatcgtattatcctgttgaatgttgatatattttagttactatttgcagTGCAAATGTTTTTGGAGTTTCAACAGAATCTATGCAGCTGTCTTTTGATGCCAGAGGAAATAGTGTTCCTACAATACTGCTGTTAATGCAAAGACATTTG
tgttgat putative branch site (score: 4)
aatgttgatatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcattgatctaggtgctttcttaatattatgtatctggtggatgcatactgaatcgtattatcctgttgaatgttgatatattttagttactatttgcagTGCAAATGTTTTTGGAGTTTCAACAGAATCTATGCAGCTGTCTTTTGATGCCAGAGGAAATAGTGTTCCTACAATACTGCTGTTAATGCAAAGACATTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - -tgctttc
- - - - - - - - - - - - - - - gtatctg
- - - - - - - - - - - - - - - - - - - -ggatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt