Sequence
atgc intronic sequence ATGC exonic sequence...tttcttcctaccagtgaggcccgtataactgtttgtatgcacatgttacttatgctagtggatgtggatatttaaatgtttgtttcattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
Basic information
species | Glycine max |
transcript | GLYMA03G42090.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g45600.1 (Oryza sativa), 3'ss of exon 4
---tttcttcctaccagtgaggcccgtataactgtttgtatgcacatgttacttatgctagtggatgtggatatttaaatgtttgtttcattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
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gttattctcaaaatctatttggctttatttattttttcttgctatctacagaatttgctatttcaca-gactaatcatgtaac-ataccatc-tcttttatagATGGCCGATCCCTTGACTGCTTTGATACATGCAGTTCAAGTGATGAATTTTCTCAAGACACTTATCTTGAAGACTGTGAAGGGACGGGAAGAAACAGCTA
upper sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g48790.1 (Oryza sativa), 3'ss of exon 4
tttcttcctaccagtgaggcccgtataactgtttgtatgcacatgttacttatgctagtggatgtggatatttaaatgtttgttt-cattgt--gctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
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----------------------------gtattagaa-acaactctggattctttcgttagaaaagcatacacatacactaacctgcaatgtttgttttccagATGGCCGATCCATTGACTGCCCTGATACATGCAGTTCAGGTCATGAATTTCCTCAAGACATTGATCTTGAAGACTTTAAAGGAAAGAGAGGCAGCCGGAA
upper sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G044495_T01 (Zea mays), 3'ss of exon 4
tttcttcctaccagtgaggcccgtataactgtttgtatgcacatgttacttatgctagtggatgtggatatttaaatgtttgtttcattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
||| || | | | | | | | || | || | | || | | | || | || | | | | || |||||||||||||| |||||||| ||||| ||||| || ||||||||||| || |||||||||||||| ||| || | |||||| || | | |
------gttactgacaag-catatttgtttctctcagcgtaccttttttctct-ctcttcaaaatccgtagtctaaccacggagcattcatccctttcagATGGCGGACCCCTTGACTGCTTTGATACATGCCGTTCAAGTGATGAATTTCCTCAAGACATTGATCTTGAGAACTGTAAAAGAAAGGGAGGAGGCTGCTA
upper sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G46710.1 (Arabidopsis thaliana), 3'ss of exon 4
tttcttcctaccagtgaggcccgtataactgtttgt-atgcacatgttacttatgctagtggatgtggatatttaaatgtttgtttcattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
| | | | | || || | | || || | ||| | || | | || | | ||||| ||| || ||||||| || ||||| |||||| | || || ||||||||||||||||||||||||||||| ||||| | | || ||| |||||| || || || |
------gtcagtaataaaattgaattttcttttaatgaaacagttgattctttagttatatagttttgaatctcatgaaaatgttttgatgt----tgtagATGGCAGATCCTTTAACTGCACTCATCCACGCAGTGCAAGTGATGAACTTTCTCAAGACTTTGATCTTAATGAACCTCAAAGAAAGGGAAAACGCAGACG
upper sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0048g02830.t01 (Vitis vinifera), 3'ss of exon 5
tttcttcctaccagtgaggcccgtataactgtt-tgtatgcacatgttacttatgctagt--ggatgtgg-atatttaaatgtttgtttcattgtgctt--tgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
| ||| | || || || || | | | | | | | || | | || |||||| |||||| ||| || || | |||||||| || ||||||||||| ||||||||||| |||||||| |||||||| || |||||| ||||| |||||||||||| ||||||||| ||||| ||
-----attggcatgtgtagttaaaatggctattgtgaaattttccttctttcaagacaatttggctacagtgtaagtaaatgattgttt-attttgtttgatacagATGGCCGATCCTTTGACTGCCTTGATTCATGCGGTGCAAGTTATGAACTTCCTTAAGACACTGATTATGAAGACCCTTCAAGAAAGAGAAGAATCAGCTG
upper sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------tttcttcctaccagt-gaggcccgtataactgtttgtatgcacatgttactt-atgctagtg-gatgtggatatttaaatgtttgtttcattgtgc---tttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
|| | || || | || || | || ||| | | ||| | || | || | | | | | || |||||| | | |||||||||| |||||||||||||| | || || ||||| |||||||||||||| || ||||| ||||| || ||| | ||| ||||| | | ||
gtaagtcatcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcagATGGCCGACCCTTTGACTGCTCTTATGCACGCAGTTCAAGTGATGAACTTGCTGAAGACGTTGATACTACGAACCTTGAAAGACAGAGAGGAGGCGATAT
upper sequence: GLYMA03G42090.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S256_73V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------tttcttcctacca--gtgaggcccgtataactgtttgtatgcacatgtt---acttatgctagtggatgtggatatttaaatgtttgttt------cattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
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gtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgta-tttgcagATGGCCGACCCTTTGACTGCTCTAATGCACGCAGTTCAGGTGATGAACTTCCTAAAGACGCTGATTCTAAGAACTTTGAAAGGTAGGGAAGAGGCGATACMapped 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|57575023|gb|CX547998.1|CX547998EST: AAATGAATGCTCGCAATATTGCCATGGTTTTTGCGCCCAACATGACACAG ATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTT
genomic: AAATGAATGCTCGCAATATTGCCATGGTTTTTGCGCCCAACATGACACAGgttagccaac ... tgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTT
EST:
gi|57575266|gb|CX548241.1|CX548241EST: AAATGAATGCTCGCAATATTGCCATGGTTTTTGCGCCCAACATGACACAG ATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTT
genomic: AAATGAATGCTCGCAATATTGCCATGGTTTTTGCGCCCAACATGACACAGgttagccaac ... tgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacttatgctagtggatgtggatatttaaatgtttgtttcattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
atatttaaatgtttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcttcctaccagtgaggcccgtataactgtttgtatgcacatgttacttatgctagtggatgtggatatttaaatgtttgtttcattgtgctttgcagATGGCGGACCCTTTGACTGCATTGATTCATGCAGTGCAAGTGATGAACTTTCTCAAGACATTGATTCTGAAGACCCTTCGAGAAAGAGATAAATCAATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - cctacca
- - - - - - - - - - - - - - - - - gtatgca
- - - - - - - - - - - - - - - - - - - - -catgtta
- - - - - - - - - - - - - - - - - - - - - - - - cttatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggatg