Sequence
atgc intronic sequence ATGC exonic sequence...accgctgagagccatattgagacattatcagccacaatctgaattattatgtgaagtctttgatttgtattaccattgatgtgctgctgctcttttgcagTGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCATTGATGAAGTTGACAGCTTTTTGGGTCAGCGTCGTACAACAGATCATGA
Basic information
species | Glycine max |
transcript | GLYMA14G26420.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G26420.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0098g01260.t01 (Vitis vinifera), 3'ss of exon 2
accgctgagagccatattgagacattatcagccacaatctgaattatta-tgtgaagtctttgatttgtatt--accattgatgtgctgctgctcttttgcagTGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCATTGATGAAGTTGACAGCTTTTTGGGTCAGCGTCGTACAACAGATCATGA
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-ttgttgaaaatttggttgtaaagttgtttaattggtcttgttttaccactaccaagtgtttctctttgatctgaacgttgatct-tttctaaactct-gcagTGGCTGCTGTATTTAGCTTGGCTTACAAACTCCAACCTGCTATTATCTTCATTGATGAGGTTGATACTTTTTTGGGTCAGCGCCGGACAACAGACCATGA
upper sequence: GLYMA14G26420.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S83_145V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------------------------------------------------accgctgagagccatattgagacattatcagccacaatctgaattattatgtgaagtctttgatttgtattacc----attgatgtgctgctgctct--tttgcagTGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCATTGATGAAGTTGACAGCTTTTTGGGTCAGCGTCGTACAACAGATCATGA
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gtacaatcttttgaagcatgattccgattgttgtgtgagttttgatgggcttgatacagc-aaatgtcagatctagtaagtgacatgta-actcatatttagtatttgaagaatcacgaatggagagcccggcagtacttaacgacgaccttgatttgcagTTACGGCAGTTTTTACACTCGCCTACAAACTTCAGCCATCGATTATTTTCATTGATGAGGTGGACAGCTTTTTGGGACAGCGTCGCGTTACTGAGCACGA
upper sequence: GLYMA14G26420.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ13213 (Selaginella moellendorffii), 3'ss of exon 2
accgctgagagccatattgagacattatcagccacaatctgaattattatgtgaag-tctttgatttgtattaccattgatgtgctgctgctcttttgcagTGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCATTGATGAAGTTGACAGCTTTTTGGGTCAGCGTCGTACAACAGATCATGA
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----------------------------------------------gtatgttttgctctttcattggtagc-tgatcgaatttct--tttcttcgtacagTGACTGCTGTATTTACCTTGGCTCACAAGCTCCAGCCTTCTATCATCTTCATCGATGAAGTGGACAGCTTCTTGGGACGTCGAGGAGTTACCAGTCACGAMapped 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|16105556|gb|BI893296.1|BI893296EST: CAGGATATTTTTTCTGATGAGCAAGTGGTTTGGAGATGCCCAGAAACTCG TGACTGCCATATTTANCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCA
genomic: CAGGATATCAAACCTGATGAGCAAGTGGTTTGGAGATGCCCAGAAACTCGgtgtgtacac ... tcttttgcagTGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCA
EST:
gi|298179688|gb|HO024903.1|HO024903EST: CAGGATATCAAACCTGATGAGCAAGTGGTTTGGAGATGCCCAGAAACTCG TGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCA
genomic: CAGGATATCAAACCTGATGAGCAAGTGGTTTGGAGATGCCCAGAAACTCGgtgtgtacac ... tcttttgcagTGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatgtgaagtctttgatttgtattaccattgatgtgctgctgctcttttgcagTGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCATTGATGAAGTTGACAGCTTTTTGGGTCAGCGTCGTACAACAGATCATGA
cattgat putative branch site (score: 4)
ctgctctttt putative PPT
tttgatttgtatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
accgctgagagccatattgagacattatcagccacaatctgaattattatgtgaagtctttgatttgtattaccattgatgtgctgctgctcttttgcagTGACTGCCATATTTAGCCTAGCTCATAAGCTCCAGCCTGCCATCATATTCATTGATGAAGTTGACAGCTTTTTGGGTCAGCGTCGTACAACAGATCATGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
-ccgctga
- - - - - - - - - - - - - - cagccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctgc