Sequence
atgc intronic sequence ATGC exonic sequence...aacttagttgcattcttatttttagttttgaatgtactagctagtagtaattatcctcacgactaacttaaacgtatatgtggttatgtttgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT
Basic information
species | Glycine max |
transcript | GLYMA17G16400.4 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G16400.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G038791_T01 (Zea mays), 3'ss of exon 5
---aacttagttgcattcttatttttagttttgaatgtactagctagtagtaattatcctcacgactaacttaaacgtatatgtggttatgtttgaccggta--gGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT
|||| || || | | | | | | || || || ||||| | | | | | || || | || |||| || ||||||||| || ||||| || || | ||||||||| ||||| ||| | ||||||||||||||||| || |
acagctttagctgaatacaaaccatctgc---agctatgctgaatacatgt--ttatcttaattttcaggctgcatgttcatcttgtcatgtgcatttattacagGTGATGAATCTTATTGGAGACGTGAGAGGAAAAGTGGCTGTTATGATGGATGATATGATCGACACAGCAG------------------------------
upper sequence: GLYMA17G16400.4 (Glycine max), 3'ss of exon 5
lower sequence: AT2G35390.3 (Arabidopsis thaliana), 3'ss of exon 4
aacttagttgcattcttatttttagttttgaatgtactagctagtagtaattatcctcacgactaacttaaacgtatatgtggttatgtttgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT
| || ||| | || | | || | | | || | | |||| | || || |||| || | |||| |||||||| ||||||||||||| ||| || || || ||||||| ||||||||||| || |||||||
-------gtatccctttctttcagagtcagagtttgctcaccaacaccgcttgcttcccc-------ttaagttcacatttg-ttatactttcctttcagGTCATGAACCTAATTGGTGATGTAAGAGGGAAGGTGGCAATAATGGTGGATGATATGATTGATACTGCTG------------------------------
upper sequence: GLYMA17G16400.4 (Glycine max), 3'ss of exon 5
lower sequence: Vv02s0012g00530.t01 (Vitis vinifera), 3'ss of exon 5
aacttagttgcattcttatttttagtt-ttgaatgtactagctagtagtaattatcct-cacgactaacttaaacgtatatgtggttat-gtttgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT
| ||| | | || || || | |||||| | | || || |||| | | | | | ||| |||| |||| | |||||||||| |||||||||||||| |||||||||||||| || ||||| ||||| ||||| || |||||||
agctttgaag-atatggatggaaagatgttgaattcttttctttgt--tacttatgagatgtcattcctggagtcaagtctgtatttattgtttaccttacagGTGATGAATCTGATTGGTGATGTCAAAGGAAAAGTTGCAGTCATGGTGGATGACATGATTGATACTGCTG------------------------------
upper sequence: GLYMA17G16400.4 (Glycine max), 3'ss of exon 5
lower sequence: PP1S403_8V6.1 (Physcomitrella patens), 3'ss of exon 4
aacttagttgcattcttatttttagttttgaatgtactagctagtagtaattatcctcacgactaacttaaacgtatatgtggttatgtt---tgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT
| ||| | | || || | || || | | | ||||| | | || || | | ||||| ||| | |||| |||||||| || || ||||| ||||||||||| ||||| ||||| || || ||||| ||||||||||
--tcaatttgaaaatgtgttctttacagcggattgaccctatgatgg-aattaaaagttggtttggattgccgttactgaagttgatgttgaacgacgtgcagGTTATGAACCTCATCGGAGATGTGAAAGGAAAAGTGGCTGTTATGGTTGACGACATGATAGACACTGCTG------------------------------
upper sequence: GLYMA17G16400.4 (Glycine max), 3'ss of exon 5
lower sequence: PP1S123_105V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------------------aacttagttgcattct-tatt-tttagttttgaatgtactagctagtagtaattatcctcacgactaact---taaacgtatatgtggtt-atgtttgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT
| || | |||| || ||||| | | | | | | | || | || | |||| ||| |||| || || ||||||| | |||||||||||||||| || ||||| || ||||| || || || ||| | ||||||||||| ||||||||||
gtgaattggcatcagcatccgcaccatctctaatgcactttgttttgtggatacaccctgcatgaccacttactcttccatggtgtaatttcctactgtatagttgatgtcatttggcatcatttagagctaagtatgtttcttgacggaaa--aatcttgtatcaaactgaccaaagaaatatttgattcatgtttggc----agGTGATGAACCTGATCGGAGATGTCAAGGGAAAGGTAGCAGTTATGCTTGATGATATGATTGACACTGCTG------------------------------Mapped 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|26045611|gb|CA783146.1|CA783146EST: GACAAGAGGCGCCCCT-TACACAATGTTGCTGAG GTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGAT
genomic: GACAAGAGGCG-CCATGGACACAATGTTGCTGAGgtaataacgg ... tgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtaattatcctcacgactaacttaaacgtatatgtggttatgtttgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT
taacttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacttagttgcattcttatttttagttttgaatgtactagctagtagtaattatcctcacgactaacttaaacgtatatgtggttatgtttgaccggtagGTGATGAACCTGATTGGTGATGTAAAAGGAAAAGTTGCTGTAATGGTAGATGATATGATCGACACTGCTGGTATGCCATCGTCATTGTCCAATTTGAACT
- - - - -gcattct
- - - - - - - - - - - - - - - aatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggttatg