Sequence
atgc intronic sequence ATGC exonic sequencegtaactcctccgttaaaccctaatctctctctcttccttctattttctattccccgcagccacgatcactctaacttttcagattcgccttccaaattcctaattgattcggatccaatttcgattcgtcgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
Basic information
species | Glycine max |
transcript | GLYMA01G36870.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 3'ss of exon 1
gtaactcctccgttaaaccctaatctctctctcttccttctattttctattccccgcagccacgatcactctaacttttcagattcgccttccaaattcctaattgattcggatccaatttcgattcgt-cgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
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---------------------------------------------gtaaggcccgccaaaccctagctccctcggtctgtgactgccccctctcgcttatcatctgccccg-atcgg----caattcgtgcgcagGATTCGAACAACCTCAAGGATGCGCTCAAGTACTCGGCGCAGATGCTCTCCGAGCTGCGGACCTCGCGGCTCTCGCCGCACAAGTATTATGATCTAT
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G17790.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaactcctccgttaaaccctaat-ctctctctcttccttctatt-ttctattccccgcagccacgatcactctaacttttcag-----attcgccttccaaatt--------cctaatt---gattcggatccaatttcgattcgtcgc---------agGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
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gtaaattctgcttttcccttcacttcttcctttcgtttctctgtgactattttcgttgaaattgagaaatttccaaatttgtacttttcattgatgtgtagaattgaaggaaccctaattttggttttgggaaaaaacttgtcttgtttttggttaattagGACTCGAATAATCTGAAAGATGCTCTCAAGTATTCGGCTCAGATGCTAAGCGAGTTACGGACTTCGAAGCTATCACCTCACAAGTACTATGATCTAT
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G51310.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaactcctccgttaaaccctaatctctctctcttccttctattttctattccccgcagccacgatcactctaacttttcagattcgccttccaaattcctaattgattcggatccaatttcgatt----cgtcgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
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----------------------gtaccactccttcccctctcctctcttcttcatcaatcaattttccattcgggatcttagaacc-----ctaaatcctgcattgttttctaacgaatctccaatttatcctcgcagGACTCCAACAATCTCAAAGACGCTCTAAAGTTTTCTGCTCAAATGCTCAGCGAGCTTCGTACTTCCAAGCTTTCTCCTCATAAATACTATGAACTCT
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03870.t01 (Vitis vinifera), 3'ss of exon 1
gtaactcctccgttaaaccctaatctctctctcttccttctattttct-----attccccgcagccacgatcactctaacttttcagattcgccttccaaattc---ctaattgattcggatccaatttcgatt-cgtcgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
||||| | | | | | | | || | | || || ||| || || | | | ||| || ||| | |||||| ||| | ||| || | || ||||||||||||||||| |||||||| | || || |||||||||||||| |||||||| | ||||| | ||| || ||||| || |||||||||||||
gtaacacgctctccttctctacctatgtttggtttgacggaagatagaggaaaatgttccccagattcgttccttttttccttttttccctttctgagaaacgcagcctaattttttcccttttttttttttttacttctcagGACTCGAACAATCTGAGGGACGCCCTCAAATACTCGGCTCAGATGCTTTCCGAGCTTCGTACTTCGAGGCTCTCCCCTCATAAATACTACGAACTAT
upper sequence: GLYMA01G36870.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S456_14V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaactcctccgttaaaccctaatctctctctcttccttctattttctattccccgcagccacgatcactctaacttttcagattcgccttccaaattcctaattgattcgga----tccaatttcgattcgtcgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
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--------------------------------------ggaatctcaaaatgctaccagatgcaatacttgtgtcacaggtcatgctcctgcagaaaacaaaggagactaagcaattttttattatgtttgactgcagGATAGCAATAATTTGCGAGAAGCTCTTAAGTATTCGGCTCAGATGTTGTCTGAGCTGAGGACGTCCAAGCTGTCACCACAAAAGTACTATGAGCTCTMapped 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|207818515|gb|GD791092.1|GD791092EST: CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTG GACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCC
genomic: CCGGAATCGCCGGCCTTCAGCAGAATTCCTTCTACATGCACCGTGCATTGgtaactcctc ... ttcgtcgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagattcgccttccaaattcctaattgattcggatccaatttcgattcgtcgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
taattgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactcctccgttaaaccctaatctctctctcttccttctattttctattccccgcagccacgatcactctaacttttcagattcgccttccaaattcctaattgattcggatccaatttcgattcgtcgcagGACTCGAACAATCTCAGGGACGCTTTGAAGTATTCGGCTCAGATGCTCTCCGAGCTCAGGACTTCCAAGCTTTCGCCTCACAAGTACTACGAACTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT