Sequence
atgc intronic sequence ATGC exonic sequence...gaattgtatataagttttgcggtcctttgacaatattcagaaatggaagttatgaatggttatggaaggtttatgacattgataagtttattatatacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC
Basic information
species | Glycine max |
transcript | GLYMA12G10030.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G10030.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0009g00410.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------------------gaattgtatataagttttgcggtcctttgacaatattcagaaatggaagttatgaatggttatggaaggtttatgacattgataag----------tttattata-tacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC
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gtatattgtatttactggcaatggcatgcatgtttcagttcagcttgcattatggttttgtggtgggttgggatagttctcaagttccagccttgcctgttggggagtgctactgtgtgcctgaaataatttaattggattttttactttgcaaagaaacatctaactttttgcagtgcagGTGTCAAACTGGTTCATAAATGCTCGGGTTCGACTGTGGAAGCCAATGGTTGAAGAAATGTACTTGGAGGAAATAAAGGATCAGGAGCACAATGGTTCCC
upper sequence: GLYMA12G10030.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S220_67V6.1 (Physcomitrella patens), 3'ss of exon 4
gaattgtatataagttttgcggtcctttgacaatattcagaaat--ggaagttatgaatggttatggaaggtttatgacatt--gataagtttattatatacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC
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--cctccactccagaacgcttgaacagtgagaagat-cagtcatcaggtagcagaaaatgaatatctgaa-tctacgatgttttgttgacttgcatgcgagcagGTTTCTAATTGGTTCATCAACGCACGAGTACGGCTGTGGAAGCCAATGGTAGAGGAGATGTACGTAGAGGAACAAAAAGAGTACCCTGGAGATCATACTG
upper sequence: GLYMA12G10030.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S258_6V6.1 (Physcomitrella patens), 3'ss of exon 4
--gaattgtatataagttttgcggtcctttgacaatattcagaaatggaagttatgaatggttatggaaggtttatgacattgataagtttattatata--cagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC
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ccagtatccagaacgcttttgttaaacatccacttttgtcaga----ggggatagaattacttgcagatggcttgacagagttacgtgacttctgtgaaatcagGTCTCTAACTGGTTCATCAACGCACGAGTTCGATTATGGAAGCCAATGGTAGAGGAAATGTACGTGGAGGAACAGAAAGAGTACTCCGAAGATCATTCTA
upper sequence: GLYMA12G10030.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24138 (Selaginella moellendorffii), 3'ss of exon 6
gaattgtatataagttttgcggtcctttgacaatattcagaaatggaagttatgaatggttatggaaggtttatgacattgataagtttattata-------tacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAA---CAAGAGCCAAACAATAGCTCCC
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----------------------------gtgcgtgctttaaaa--aaagcttt---tgtcctcggaagcttcttgttgtggcttaacttgctgtggaatctctgcagGTCTCCAACTGGTTTATTAATGCCCGAGTCCGGCTCTGGAAGCCTATGGTCGAGGAAATGTATCAGGAGGAGATTAAAGAGCAGGAGCTCGG-GGTGGCGT--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|21677523|gb|BQ629874.1|BQ629874EST: ACTCCGATAAGGTTATGCTTGCAAAACAAACTGGGCTTACTCGGAGCCAG GTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTA
genomic: ACTCCGATAAGGTTATGCTTGCAAAACAAACTGGGCTTACTCGGAGCCAGgtatatttca ... ttatatacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaagttatgaatggttatggaaggtttatgacattgataagtttattatatacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC
cattgat putative branch site (score: 4)
tttatgacattgataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaattgtatataagttttgcggtcctttgacaatattcagaaatggaagttatgaatggttatggaaggtttatgacattgataagtttattatatacagGTATCTAACTGGTTTATAAATGCCCGAGTTCGGCTATGGAAGCCAATGGTAGAAGAAATGTACTTGGAAGAGGTAAAACAAGAGCCAAACAATAGCTCCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - tcctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggaagg