Sequence
atgc intronic sequence ATGC exonic sequence...ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
Basic information
species | Glycine max |
transcript | GLYMA01G29470.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g28180.3 (Oryza sativa), 3'ss of exon 2
ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatct-agatgttaacttat----ttctgtgccttatttattcac-agATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
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---------------gtaaactcctcttttttttttggtatatgcaaatg-taatgcttatttgagatatccatatttaacctgctctaatttttgttttcaccagATGGCTGAATATAGGATTTCAATCTATGGGAGGAAGCAAAGTGAATGGGACAACCTTGCAAGCTGGATAGTGAACAATGAATTGTCCAGTGAAAATGTTG
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G416667_T01 (Zea mays), 3'ss of exon 10
ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttat--tcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
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----gtaaactgtcagctggataacttttttagtttttaattcagaagtactt---cttattt-gatatcttgttactt-tatccctaatatgctatttcagATGGCAGAATATAGGATTTCAATCTACGGAAGGAAACAGAGTGAATGGGACCAACTTGCAAGTTGGATAGTGAACAATGAATTGCACAGTGGAAATGTTG
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: AT2G38280.1 (Arabidopsis thaliana), 3'ss of exon 10
-ttggacttgttgacaataatttacca-----tttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
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catggcattgctca-aattctgtgtcaagaaatcttcttgccaaagcagatccataattgctctgtttt--gtttttcctgatgtctacg--ttgaacact-gcagATGGCTGAATACAGAATATCTATATATGGCAGAAAAATGAGCGAGTGGGACCAACTCGCTAGTTGGATTGTGAACAATGATCTATACAGTGAGAATGTTG
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 3'ss of exon 10
ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatctagatgt-taacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
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-agggaatcttcatctgcatgtgtatgagcccatctgtttttgatttatttgtttatttattatggtttgtaaattcctgatgctaaatgctatgctacagATGGCTGAATACAGGATATCAATATATGGCAGAAAGCAAAGTGAGTGGGACCAACTTGCCAGTTGGATAGTGAATAATGATTTGTACAGTGAGAATGTTG
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------------------------------ttggacttgttgacaat---aatttaccatttcttgactgtagtttatatatgctcatccccatctagatg-------------ttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
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gtaaacatctacaacttcttttcaattaaatttttttattagatgtttttgtactccattttgaaataccacttctgcccaattcacaaccccaccacacaaggttttgagtgagcaacacacatgggttttgagtttttgaggggcatgaagtccattgaatcccatcaacagcatattcactttcagATGGCAGAGTATAGAATTTCTATCTATGGGAGGAAGGAAAGTGAATGGGACCAGTTAGCCAGTTGGATTGTCACTAACAAACTTCAAAGTGAGAATGTGA
upper sequence: GLYMA01G29470.2 (Glycine max), 3'ss of exon 11
lower sequence: PP1S77_89V6.1 (Physcomitrella patens), 3'ss of exon 10
-ttggacttgttgacaataat-ttaccatttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
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tgaaaacctcctgtctatgttgctagtactctttatctttaaaactaaaatccttccacttgcaaagaatcatgacgatatttgtctgttcgttgt--gtagATGGCTGAGTATAGGATATCAATTTACGGAAGGAAGAAGAGTGAGTGGGATCAACTGGCCGATTGGATTGTTCACAATAAGCTGCACAGTGAGAACGTCAMapped 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|7925052|gb|AW831078.1|AW831078EST: GTGAGTTAACTAAGCAAGTGTTTTCAGATCTTGCTGCCAGTAAATATCAG ATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGAC
genomic: GTGAGTTAACTAAGCAAGTGTTTTCAGATCTTGCTGCCAGTAAATATCAGgtgctttctt ... ttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGAC
EST:
gi|254332340|gb|GR846385.1|GR846385EST: GTGAGTTAACTAAGCAAGTGTTTTCAGATCTTGCTGCCAGTAAATATCAG ATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGAC
genomic: GTGAGTTAACTAAGCAAGTGTTTTCAGATCTTGCTGCCAGTAAATATCAGgtgctttctt ... ttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
tgttaac putative branch site (score: 2)
ccttattt putative PPT
atgttaacttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttggacttgttgacaataatttaccatttcttgactgtagtttatatatgctcatccccatctagatgttaacttatttctgtgccttatttattcacagATGGCTGAATATAGAATATCAATATATGGTAGGAAGCAAAGTGAGTGGGACCAACTAGCCAGTTGGATAGTGAATAATGATTTGTACAGCGAGAATGTCG
- - - -tgttgac
- - - - - - - - - - - -ccatttc
- - - - - - - - - - - - - - - ttgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtgc