Sequence
atgc intronic sequence ATGC exonic sequence...agaaatggtgggactgtgggaggtgcattctgtttttttgtgcattacaaattccaggttttaatttgatgccttttctatctgatcttcaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA19G35390.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G35390.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G171620_T02 (Zea mays), 3'ss of exon 1
------------------------------agaaatggtgggactgtgggaggtgcattctgtttttttgtgcattacaaattccaggtttta----atttgatgccttttctatctgatcttca-----attttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
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gtaagacctcagctagtgttaatcaacaagtgccatcatacaattcttgca--tgcacttttgatgatggtgatttaaacagttaatgttgtgctatatattatggatcatctgattcattttcccacatgctctgcagGTACGTTGCCCCAGAGTATGCGATGACAGGGCATCTGCTTGTCAAGAGCGACGTCTACAGCTACGGAGTGGTGCTCCTGGAGCTGCTGTCAGGCCGAAAA
upper sequence: GLYMA19G35390.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv07s0005g04710.t01 (Vitis vinifera), 3'ss of exon 4
agaaatggtgggactgtgggaggtgcattctgtttttttgtgcattacaaattccaggttttaatttgatgccttttct---atctgatcttcaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
| | || | | | ||||| | | | ||| | | ||| || | ||| | | |||| || | | | |||||||||||||||| || |||||||| ||||| || ||| |||| |||||||||||||| || |||||||| || ||| ||||||| |||||| | || |||||
-catttaatgcg--tattttaggtgtttgtttgtgccatgtatctcaagaatggcaagcttttaacacttttctttgtggggatttaaattgtttatttgcagGTATGTTGCTCCTGAATATGCAATGACGGGGCATCTACTTGTCAAAAGTGATGTATACAGTTATGGGGTCGTGTTGCTTGAGCTTCTCTCTGGAAGAAAA
upper sequence: GLYMA19G35390.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S343_14V6.1 (Physcomitrella patens), 3'ss of exon 7
agaaatggtgggactgtgggaggtgcattctgtttttttgtgcattacaaattccag-gttttaatttgatgccttttctatctgatct-tcaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
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--ttctcttgtattctcgtttcttctattttttagatatctttggctggaccgctagcgttgttacttgattcctgcacttactgattgatttctactgcagGTATGTGGCCCCTGAATACGCAATGACAGGGCATCTACTTGTGAAGAGTGATGTTTACAGTTACGGAGTAGTGCTTCTAGAGCTCCTCTCTGGACGGAAA
upper sequence: GLYMA19G35390.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S43_35V6.1 (Physcomitrella patens), 3'ss of exon 2
agaaatggtgggactgtgggaggtgcattctgtttttttgt-gcattacaaattccaggttttaatttgatgccttttctatctgatcttcaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
|| | | | | ||| |||| | | || || || ||| | | || | | | ||||||||||| ||||| || || || |||||||| |||||||| || || |||||||||||||||||||| || ||||| || || || || | || ||||
-ctttcaccttcacatctgaatatttaggatgtattttgaccagactggtaaggttgtgtcttgattattgacttacggtagtagttgatttcaactgcagGTATGTGGCCCCGGAGTACGCTATGACAGGGCATTTACTTGTGAAGAGTGATGTTTATAGTTATGGAGTGGTGCTTCTGGAGCTCCTTTCTGGACGAAAAMapped 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|298198470|gb|HO040009.1|HO040009EST: GCAACTGAAGGAAGTAATCATATTTCAACGCGGGTGATGGGAACTTTTGG GTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGA
genomic: GCAACTGAAGGAAGTAATCATATTTCAACGCGGGTGATGGGAACTTTTGGgtaagtgtat ... aattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tacaaattccaggttttaatttgatgccttttctatctgatcttcaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
ttttaatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaaatggtgggactgtgggaggtgcattctgtttttttgtgcattacaaattccaggttttaatttgatgccttttctatctgatcttcaattttgcagGTATGTTGCCCCAGAATATGCGATGACAGGCCATTTACTCGTCAAAAGTGATGTTTATAGTTATGGTGTTGTGCTGCTTGAACTTCTCACAGGCAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - -tggtggg
- - - - - - - -gtgggag
- - - - - - - - - - - - gcattct
- - - - - - - - - - - - - - - - - - - - -gcattac