Sequence
atgc intronic sequence ATGC exonic sequence...tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
Basic information
species | Glycine max |
transcript | GLYMA17G08300.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g55250.1 (Oryza sativa), 3'ss of exon 4
--tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
|| | | || ||| | || | || | || || | | | || | | || | | || | | | ||| ||||| |||||||| || ||||| || |||||||| ||||||||||||||||| |||||||||||||||
catccatcttcatatcttagctgatagggttgctccagcacaaagtagagtgacacggatcactgtcac-tgaaatgacgatgtggaatttcgttttg-cagACCGACAAGGCATCGATGCTCGACGAGATCATTGATTATGTGAAGTTCCTCCAGCTCCAAGTCAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os09g25040.1 (Oryza sativa), 3'ss of exon 4
tcaacatctatctctcttttagt-----attaaaaat--acacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtgga-ttga--cagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG-------------------------
| || | ||| ||| ||| | || || | | | | ||| | | ||||| | | | || |||| |||| ||||| |||||||| ||||||||||| ||||||||||| || || ||||||||||| ||||||||||||
-cgacgctcgctttcttttcagttccccatttgagattaacctcttcgtgaattgctcatctcatctcaagtgtgtgtgtgtgtgtgtgtctttcttggagTTGATGCAGACGGACAAGGCTTCCATGCTGGACGAGATCATCGACTACGTCAAGTTCCTACAACTCCAAGTCAAGGCAAGCACGTACACTAAATTACTAA
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g08500.1 (Oryza sativa), 3'ss of exon 3
---------tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
|| | || | | | || | | | || | ||| | || | ||| | |||| ||| ||| | | | ||| ||||| |||||||| || |||||||| ||||||||||| || || |||||||| |||||||||||||||
tgggcgcattcgtgcccaattttgtcatcgtttttcttgacatcttgatgaagaaaatga-----agtgattgaatg-gagttctttgatttgatt--ttgcttg-cagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTGCAGCTCCAAGTCAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G027563_T02 (Zea mays), 3'ss of exon 3
tcaacatctatctctcttttagtat--taaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
| | || ||| |||| || | | | || | | || | || || | | | | || |||| || ||||| |||||||| || |||||||| ||||||||||| || || ||||||||||||||||||
ttgcgcttgctcactcaccgagtacagtactgaactattgatccatcttgctctgtgttttctcaatatcttggattggatgcctgcgccgtgcat--gcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAAGTTCCTACAGCTCCAA------
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G350165_T01 (Zea mays), 3'ss of exon 4
----tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
|| || | | | | | | | | | ||| || | | || | ||| || || || || ||||| |||||||| || |||||||| |||||| |||| || || |||||||| |||||||||||||||
cttgtcgtaatgtcgtccaccctctatcctccttttcgttcttcgcgcttgacttcctc-gccgacgactgatccat-catctcaatgtcttgt--atctgcagACGGACAAGGCGTCGATGCTGGACGAGATCGTCGACTACGTCAAGTTCCTTCAGCTCCAAGTCAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G316758_T01 (Zea mays), 3'ss of exon 3
tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttctt-ccattgttaaaatatgtgt------tcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
| | | || | | ||||||| |||| | | || | || || ||| |||| | | | | || ||| ||||| |||||||| || ||||| |||||||| || || || ||||||||||| |||||||||||||||
------cgtctttgatcgacagagcttccatggcacaaactaataagactcattgtcgctgaaaacgatcgtgccgtgtgtcatcgtatggaattttgttttg-cagACCGACAAGGCATCGATGCTTGATGAGATTATTGACTACGTGAAGTTCCTCCAGCTCCAAGTCAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G067654_T01 (Zea mays), 3'ss of exon 4
-----------------------tcaacatctatctctcttttagtattaaaaatac--acaaacaa-atacaat-ttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
| | || ||||| | | | |||| ||| | |||| | | | || || | | | | | |||| || ||||| |||||||| || |||||||| ||||||||||| || || | |||| | |||||||||||||||
gtcggcatcccccctctagctagctagctcctttctcttctctctcgctcgcgtcgtcaacaatcaacagacaacactgaaatggcgacgtggtgtgggtcggtcgtcgttgtttgtggttttgcagACGGACAAGGCGTCGATGCTGGACGAGATCATCGACTACGTCAGGTTCTTGCAGCTCCAAGTCAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G24260.1 (Arabidopsis thaliana), 3'ss of exon 3
tcaacatctatctctcttttagtattaaa-aatacacaaacaaatacaatttcttc-cattgttaaaatatgtgttcattgggttggctcgtg----gattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
| | | || |||| ||| || || |||| | || || | | | | | |||| | || | || || ||||||| |||||||| || ||||| ||||||||||| |||||||| ||||| |||| ||||||||||||
------taggctacaataataaagttaactaatgcagtaataaatgagttaggatctcagttctgacagttttgtttttgtattttatttgtataataatggacagACAGACAAGGCATCGATGCTCGATGAGATCATAGATTATGTCAAGTTTTTACAACTCCAAGTCAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G30980.1 (Arabidopsis thaliana), 3'ss of exon 3
-------tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
| || |||| | || || ||| | | | ||||| || || | | || | | | || |||| | | ||| |||||| ||||| || || ||||| |||||||| ||||||||||| |||||| |||||||||||||||||
tagctaattaat-tctaaaatttaattgataataatacttaataaacagatgcagaatt----gctaacaaggttt-tttttattgttaaaaataata-attaacagACAGACAAAGCATCAATGCTCGATGAGATTATCGATTATGTCAAGTTCTTACAGCTCCAAGTCAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0037g00040.t01 (Vitis vinifera), 3'ss of exon 4
tcaacatctatctctcttttagtattaaaaat-acacaaacaaatacaatttcttccattgttaa---aatatgtgttcattgg-gttggctcg--tggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
| |||| ||| | | | | | | || | | || ||| ||| |||| | || | ||||| | | |||| |||||||| |||||||| || ||||||||||||||||| || ||||| || ||||| ||||||||||| |||
-------cccggtctcgagcagtgcggcgagtcatgcgtagcgaaaccacctattttatttttactttaatacgaaatcgataatgttgggtggggtggaatgacagACGGACAAGGCTTCAATGCTGGATGAGATCATTGACTATGTCAAATTCCTGCAGCTCCAAGTGAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S209_22V6.2 (Physcomitrella patens), 3'ss of exon 3
-----------------------------------------------------------------------------------------tcaaca-tctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
|| | | ||||| ||| | || | | |||| | ||| ||| | | ||| || | | | || || || ||| ||||||||| ||||| || ||||||||||| |||||||| ||||| |||||||| || || ||||| |||
gtgcggcatcgttcgaacctgcctttcacttttttgtgctctgaatcagttgtatatgtatggtttagccacgtggtgaaaacataggtgcattagtgtatctttctctacctacttatg-tacagcatgaaagacagatgaagtctttgcta---tttaatcttatctcactg--ctgtttattaacagACTGATAAGGCGTCTATGCTGGATGAAATCATCGACTATGTCAAGTTCCTGCAACTTCAAGTGAAG
upper sequence: GLYMA17G08300.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S173_83V6.1 (Physcomitrella patens), 3'ss of exon 3
tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaat-atgtgttcattgggttg--gctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
|| | | | | |||| || || | || | | | | |||| || || | || | |||||| |||||| || ||||| || ||||||||||| ||||||||||| || |||||||| || |||||||| |||
-gaaacttcgtgtatttttttcatctactttcacttgggcttattttaaaatctaattagaagaaatgatccaatcctcttactgctgtctgtggat--acagACGGATAAGGCGTCGATGCTGGATGAAATCATCGATTACGTCAAGTTCCTGCAACTCCAAGTAAAGMapped 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|10710098|gb|BF009822.1|BF009822EST: TCGCAGAGCGAATGAAGGCCCTACATGAACTAGTTCCTAATGCCAACAAG ACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTA
genomic: TCGCAGAGCGAATGAAGGCCCTACAAGAACTAGTTCCTAATGCCAACAAGgtaaacaatc ... ggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTA
EST:
gi|254343140|gb|GR859302.1|GR859302EST: TCGCAGAGCGAATGAAGGCCCTACAAGAACTAGTTCCTAATGCCAACAAG ACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTA
genomic: TCGCAGAGCGAATGAAGGCCCTACAAGAACTAGTTCCTAATGCCAACAAGgtaaacaatc ... ggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
attgttaaaatatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaacatctatctctcttttagtattaaaaatacacaaacaaatacaatttcttccattgttaaaatatgtgttcattgggttggctcgtggattgacagACTGACAAGGCCTCCATGCTGGATGAGATCATCGATTATGTGAAGTTCCTACAGCTCCAAGTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
-caacatc
- - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - -cacaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggttgg