Sequence
atgc intronic sequence ATGC exonic sequence...actgctagctaggtagtttcagttatttactaaaaggtatcatgattctgttatgcttctcggaaagtgtgtgtgcctaactatgttcaatatgatgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
Basic information
species | Glycine max |
transcript | GLYMA20G09810.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 6
actgctagctaggtagtttcagttatttactaaaaggtatcatgattctgttatgcttctcggaaagtgtgtgtgcctaactatgttcaatatga--tgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
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---------------gtatgttacatctatca-----tatcatgtttgcaacatagttaattaattgtgaaattatggttttaatattgatgtggactacagGAAATCCAAGAGTCACACCAGAGGTTACAAGGGACGTATGCCTGTTAGCTAGAATGATGGCTGCTAACTTATACTATGCACAGATAGAGGATCTGATGTT
upper sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G110714_T01 (Zea mays), 3'ss of exon 4
--------actgctagctaggtagtttcagttatttactaaaag-gtatcatgattctgttatgcttctc--ggaaagtgtgtgtgcctaactatgt-tcaatatg-atg-cagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
| || || | ||| | | || | | | | || || | | | ||| | | || ||| ||||| || || | ||| |||| ||||||||||| || || || || || || ||||| ||||| ||||||||||||||||||||||| ||||| | |||||||||| || || |||||
gtacatagcattctctctcccttatttggatagtatatttgatgtgctgaatcatgcaactgtagttcacaagaaagaagtgcaaatataactctgaactgatgtccatgacagGGAATCCAAGAGTCACGCCAGAGGTTACAAGGGATGTATGCTTGTTGGCTAGAATGATGGCTGCTAATTTGTATAATGCCCAGATAGAAGACCTGATGTT
upper sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G473001_T02 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------actgctagctaggtagtttcagttatttactaaaaggtatcatgattctgttatgcttctcggaaagtgtgtgtgcctaactatgtt-caatat-------gatgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
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gtgagtgacacatctctacatatttgtcttgtcttctcatggcattatattaaatatgcagtatttgcagcacctattattatctttgtttctagtggttaggaagatgattattcattgtgcctgtgtctgcggtttgcacctctgtcctattctaaagcaatgtctctacaaatgcagGAAATCCAAGAGTGACACCAGAGGTTACCAGGGATGTCTGCTTGCTTGCCAGAATGATGGCATCAAACTTGTACTGCTCTCAGATTGAGGATCTCATGTT
upper sequence: GLYMA20G09810.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 4
------actgctagctaggtagtttcagttatttactaaaaggtatcatgattctg--ttatgcttctcggaaagtgtgtgtgcctaactatgttcaatatgatgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
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taatttatcaaagttgagtcagactcattagttgactaccagttatagaaagcaggactctctctcccctggattaacatgcttttgac--------atgaaatgcagGTAACCCAAGGGTGACTCCTGAGGTCACAAGGGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTATACTATTCCCAGATAGAGGATCTTATGTTMapped 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|151396752|gb|EV266625.1|EV266625EST: TAATGCTCCTCTCATTCAATTTTCTTCTTGGATGGGTGGAGATCGTGATG GCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTA
genomic: TAATGCTCCTCTCATTCAATTTTCTTCTTGGATGGGTGGAGATCGTGATGgtaggttctt ... tatgatgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttctgttatgcttctcggaaagtgtgtgtgcctaactatgttcaatatgatgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
gcctaac putative branch site (score: 2)
ttcaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actgctagctaggtagtttcagttatttactaaaaggtatcatgattctgttatgcttctcggaaagtgtgtgtgcctaactatgttcaatatgatgcagGCAATCCAAGAGTAACTCCTGAAGTGACCAGAGATGTTTGCTTATTGGCTAGAATGATGGCTGCTAACTTGTACTACTCCCAGATAGAGGATCTTATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
actgcta
- - - - - - - - - - - - - - - - - - - - - -gattctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtg