Sequence
atgc intronic sequence ATGC exonic sequence...ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
Basic information
species | Glycine max |
transcript | GLYMA07G38770.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38770.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 3'ss of exon 3
ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttcct----tttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
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---tgatgcccaaacag-aggtatattgttattcactatgtactgtaccaaactcagtatattcagtgcagtgctatagtgctaatatgtaattgcaattgcagAGTATGACTCAGATGACAAGCCAATCCCTGAGACGCTTAAACCTATGGTCGATGGTGGGACTGAAGGTTTCAAAGGTCATGCTAGAGTCATCATACCTGG
upper sequence: GLYMA07G38770.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G19180.1 (Arabidopsis thaliana), 3'ss of exon 3
ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
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------------gtatgcaaattc---tttaacctttaatactttatccct-cggctttttgaagttctctgt--ctgataatgtgcttgtgaaatgtagAGTATAATGAAGATGATACTCCGAAAAGAGAAACGATCAAGCCAATGGTAGATGGGGGAACTGAAGGTTTCAAGGGTCATGCTAGAGTTATCTTGCCTGG
upper sequence: GLYMA07G38770.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g02820.t01 (Vitis vinifera), 3'ss of exon 3
-ctattatgtagaatttccatctctacatt-cagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
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gcttttgagaatcaaatgtgtgtcattttcatagtgagtagatttttctacattctgcctcatcttatct--agtcgtctcattgtgtttttggaaatttagAGTATGATTCTGATGATAAACCACTGGAAGAAACAATTAAACCTATGGTGGATGGTGGAACTGAAGGCTTCAAGGGTCATGCCAGGGTTATCATTCCAGGMapped 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|298187660|gb|HO034809.1|HO034809EST: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAG AGTACGATTCTGATGA
genomic: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAGgtctgttttc ... ataaatctagAGTACGATTCTGATGA
EST:
gi|254322096|gb|GR837510.1|GR837510EST: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAG AGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGG
genomic: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAGgtctgttttc ... ataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGG
EST:
gi|17024070|gb|BM095104.1|BM095104EST: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAG AGTACGATTCTGATGATAA
genomic: TTCCATTGAGGCCCGCAGTTATATCAATACTGTTGCCTGCAGTTTTCTAGgtctgttttc ... ataaatctagAGTACGATTCTGATGATAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
tactgat putative branch site (score: 2)
ttttactgataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctattatgtagaatttccatctctacattcagtcccaaagatttggtgcagactgcttatgctaattttcagtttcttttccttttactgataaatctagAGTACGATTCTGATGATAATCCACAAGAAGAGACAATCAAACCTATGGTGGATGGTGGGACTGAAGGTTTCAAGGGCCATGCTAGGGTTATCATGCCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - tatgtag
- - - - - - - - ccatctc
- - - - - - - - - - - - - - -cagtccc
- - - - - - - - - - - - - - - - - - - - - - - tgcagac
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg