Sequence
atgc intronic sequence ATGC exonic sequencegtattgctgtataaaagtattgcatagtagttcatgactgaagtctgtttccttttaatatgtgcacaatttacaaatggtactcactgcagGTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTGTTTTGAGTTGACCCTGGAAATTTGTGATAATAAATGGCCCAGTGCTGCT
Basic information
species | Glycine max |
transcript | GLYMA20G31000.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31000.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g05240.1 (Oryza sativa), 3'ss of exon 10
----------------gtattgctgtataaaagtattgcatagtagttcatgactgaagtctgtttccttttaatatgtgcac-aatttacaa---atggtactcactgc--agGTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTGTTTTGAGTTGACCCTGGAAATTTGTGATAATAAATGGCCCAGTGCTGCT
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gtataaaactagttttgtattattgctccttatcattttttt-tatttcatatcaaacattttgttgctgctacttttcatgctaactagcaatctatgcttttttgtgttgagGTATCCAATCTATGGTGGGATGCAAGACTGGAACTATATACATGGAGGTTGCTTTGAGTTAACCCTGGAAATTAGTGACGTAAAATGGCCAAAGGCAGCT
upper sequence: GLYMA20G31000.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G106683_T02 (Zea mays), 3'ss of exon 10
-------------------gtattgctgtataaaagtattgcatagt--agttcatgactgaagtctgtttccttttaatatgtgcacaatttacaa-atggtactcactgcagGTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTGTTTTGAGTTGACCCTGGAAATTTGTGATAATAAATGGCCCAGTGCTGCT
| | || ||| || || | | | || | | | | ||| | || | || ||| ||| || | | ||||||||| ||||||| || ||||| || |||||||||||||||| ||||| |||||||| || ||||| ||| |||| | || ||||| | || | |
gtaaacgaacaatagcaagttcatacttcatatgagatttcctttatctaggtactaggtaggttgtgtatgtgttggctttgaat-caaacaacatcattgcttgtggtccagGTACCCAATATATGGTGGTATGCAGGACTGGAACTATATACATGGAGGCTGCTTTGAGTTAACTCTGGAGATTAGTGACACAAAGTGGCCAAAAGCAGAT
upper sequence: GLYMA20G31000.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0157g00050.t01 (Vitis vinifera), 3'ss of exon 10
---gtattgctgtataaaagtattgcatagtagttcatgactgaagtctgtttccttttaatatgtgc---acaatt--tacaaatggtactca-ctgcagGTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTGTTTTGAGTTGACCCTGGAAATTTGTGATAATAAATGGCCCAGTGCTGCT
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cggttatttttttttttaacaatcaagttgttaaaagt-acttctcttttcttctttttattttctgtttagcaattgcttcaagaaaaacttttctgcagGTACCCCATATATGGTGGCATGCAAGATTGGAACTATATACATGGTGGCTGTTTTGAATTGACACTGGAGATCAGTGACAACAAGTGGCCTAACACTATTMapped 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|57575392|gb|CX548367.1|CX548367EST: TCGGTGGAATTACAAATGGAGCCGCATG GTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTG
genomic: TCGGTGGAATTACAAATGGAGCCGCATGgtattgctgt ... ctcactgcagGTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTG
EST:
gi|57575090|gb|CX548065.1|CX548065EST: GTGGAATTACAAATGGAGCCGCATG GTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTG
genomic: GTGGAATTACAAATGGAGCCGCATGgtattgctgt ... ctcactgcagGTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgaagtctgtttccttttaatatgtgcacaatttacaaatggtactcactgcagGTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTGTTTTGAGTTGACCCTGGAAATTTGTGATAATAAATGGCCCAGTGCTGCT
tactcac putative branch site (score: 1)
tttccttttaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgctgtataaaagtattgcatagtagttcatgactgaagtctgtttccttttaatatgtgcacaatttacaaatggtactcactgcagGTACCCTCTATATGGGGGAATGCAAGATTGGAACTATATACATGCTGGCTGTTTTGAGTTGACCCTGGAAATTTGTGATAATAAATGGCCCAGTGCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT