Sequence
atgc intronic sequence ATGC exonic sequenceggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA
Basic information
species | Glycine max |
transcript | GLYMA17G37820.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 4
ggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaaca--tgctggtgc-tacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-
|| ||| || || | || ||||| || | | | | ||| ||| | | | || || | | |||||||| |||| ||||| ||||| |||||||| ||||| || || |||||||||||||| ||||| ||| | || ||||| | ||||| || || |||
-----------gtatattaaacttcgta-gctgatagtcttttttgtgtggtatatcttgttttggaaattgacttcatggcatctgctgtgggcacgtgtagATTAAGCTGGATAAGGAGAAGAAGATTCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTCATTAAGAACCTTGGGACCATTGCCAAAT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G399073_T03 (Zea mays), 3'ss of exon 4
-ggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-
| | || | || || | | | | | | || | || | | | || | | || | | ||||| ||| |||||||||||||||| || |||||||| ||||| ||||| || || |||||||||||||| ||||||||| | || || || | || || || || ||
gtaatttcaatgtcgagagaccatttttcttttgtctggc--atcatatcttgctttagacttgggcttgatggc--atctgatatatgcttatgc---agATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G110574_T01 (Zea mays), 3'ss of exon 8
ggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-
|| ||| | | | | | | | ||| |||||| | | | | | || | | ||||||||||||||||| || |||||||| ||||| ||||| || || |||||||||||||| ||||| ||| | || ||||| | || || || || |||
-----------gtagatttcaatgttgagagctgtttttttttctgt-tgggcaacgctttagaatcagacctcaaggcatctggtctatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G141931_T02 (Zea mays), 3'ss of exon 4
ggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-
|| ||| | | | | | | | ||| ||||||| | | | | | || || | | ||||||||||||||||| || |||||||| ||||| ||||| || || |||||||||||||| ||||| ||| | || ||||| | || || || || |||
-----------gtagatttcaatgttgagagctgtttttttttctgt-tgggcaatgctttagaatcagacctcaaggcatcaaatctatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G022909_T01 (Zea mays), 3'ss of exon 5
ggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-
|| ||| || ||| | || | | ||| |||||| | | | | | || | | ||||||||||||||||| || |||||||| ||||| ||||| || || |||||||||||||| ||||| ||| | || ||||| | || || || || |||
-----------gtagatttca---atgttgagagctgttttttttgt-tgggcaacgctttagaatcagacctcaaggcatctggtctatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G063988_T02 (Zea mays), 3'ss of exon 11
ggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-
|| ||| | | | | | || ||| |||||| | | | | | || | | ||||||||||||||||| || |||||||| ||||| ||| | || || |||||||||||||| ||||| ||| | || ||||| | || || || || |||
-----------gtagatttcaatgttcagagctgttttttttctgttg--ggcaacgctttagaatcagacctcaaggcatctggtctatgcttatgcagATTAAGTTGGACAAAGAGAAGAAAATCCTCTCCATTTGGGATAGGGGTATTGGTATGACCAAGGAAGATCTTATTAAGAACCTTGGAACGATTGCTAAAT
upper sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 4
ggttagtattgctaaattctggttattatgaagacagtctaaacaat-gccggcggtgctt-tattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA-
|| | ||| | | || | || | | || | | | || | |||| | || || ||| | | |||||||| || ||||||||||||||||| || |||||||| || |||||||| |||||||| ||||| ||||| || ||||| || || ||||| ||||||
-------gttagttaatatta-ctgttgtaaaaattttgtattttcttgtttataatttttctgacagtttgaattc---ttataatatgataa-aatgcagATTAAATTAGACAAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATMapped 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|208261680|gb|GE060035.1|GE060035EST: ACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA GATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTAT
genomic: ACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCAggttagtatt ... tggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTAT
EST:
gi|298170585|gb|HO019209.1|HO019209EST: ACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCA GATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTAT
genomic: ACGGATAAGGACGTTTTGGGAGAAGGTGATAACACCAAGCTTGATATTCAggttagtatt ... tggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA
aactaaa putative branch site (score: 2)
tttattgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggttagtattgctaaattctggttattatgaagacagtctaaacaatgccggcggtgctttattgttttgcaactaaactaaaacatgctggtgctacaGATTAAGTTGGACAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA