Sequence
atgc intronic sequence ATGC exonic sequence...atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattctgtcataatgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
Basic information
species | Glycine max |
transcript | GLYMA02G45540.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g47470.1 (Oryza sativa), 3'ss of exon 3
----atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattctgtcataatgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA---
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atggaaattctgttccttcccttgtgcataatcaatatgtgttttccttgttcccttgtttct---cactgt-acattgaccttttctgaatattcacctgcagGATGCTTGTCTATGAATATGTCAACAATGGAAACCTAGAACAATGGCTTCATGGGGCCATGAGTGGG---GGCATCCTTACTTGGGAAAACCGTATGAAGATT
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g41730.1 (Oryza sativa), 3'ss of exon 2
atattctactttgtccaaaattgaacataagcttttctctatgtta-tgtctctatatatgtattctgtc-ataatgaatgtgcttcccgattgata---ttcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
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-----ttcatagaactatagaagtccattaacctatatcaaactaagcttttccgtgaatctgttaggtttacagcaaaacatcattaggcttctcacgttgcagGATGCTTGTCTATGAATACATCAACAATGGGAACTTAGACCAGTGGTTACATGGCGCAAGGAGTCAACATGGTGTTCTTACATGGGAAGCCCGCATGAAA
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 1
--atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatata-tgtattctgtcataatgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
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taaagtggtgtatggacaccattcaaatatatatgcttca-tatgccatattgttatttaatctattttagcgttctcctaatcatatcatgttatt--ccagGATGCTTGTGTACGAGTATGTGAATAATGGGAACTTAGAACAGTGGCTTCATGGTGCAATGCGTCAGCACGGTGTTCTTACTTGGGAGGCCCGGATGAAA
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 3
--------atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattctgtcataatgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
|||| ||| || ||| | | | | ||| || | | | || ||| | ||| | || | | | | | |||| ||||||||||||| || ||||||||||| || |||||||| ||| | ||||| ||||| || |||| ||||| ||||| ||||| ||||||
agtggttaatatattaccatgg--aaatctatatgtttcatacatcatatattgttttttaatctatttgag-tgttctcattatcatatcctcttact-----ccagGATGCTTGTGTATGAGTACGTGAACAATGGAAATTTAGAACAGTGGCTTCATGGTGCCATGCGTCAGCATGGTGTTCTTACTTGGGAAGCCCGGATGAAA
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 2
atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattctgtcataatgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
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--------------------------gtgagtctcact-tgtctttaatccatttgagca-attggattgtactgaatctaaatataatgatgaatgcagGATGCTTGTTTATGAGTATGTTAATAGTGGTAACTTAGAACAATGGCTACATGGAGCAATGCGGCAACATGGAAATCTCACTTGGGAAGCACGGATGAAA
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattc-tgtcata-atgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
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gtgagtctgacttgtctcttatcagtctgaatgtactactaatttagtctcatgagtaatctcctattgtactaccgaatagaaacttgtcccatgtatcaatttctgttttgatgta-atgcagGATGCTTGTTTATGAGTATGTGAATAGTGGTAACTTAGAACAATGGCTACATGGAGCCATGGGAAAACAAAGCACTCTCACTTGGGAGGCTCGCATGAAA
upper sequence: GLYMA02G45540.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------------------------atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattctgtc-ataatga----atgtgcttcccgattgatatt-cagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
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gtaagatttgttcactttttattgatgtggtaatttatttcattcctattcatttggcatgttggatgttattattatttattgtcatgatgaagtactttttcgttgaaaaacaaa-gtacttttccaattcttttgcaatcttgtcgatctgatttgcctgggatgtggttatgtacttattattctttaatatagGATGCTGGTGTATGAATATGTGAACAATGGCAACTTAGAACAGTGGCTTCATGGAGCTATGCGCCAATATGGCAACCTTACTTGGGAGGCCCGCATGAAGMapped 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|6481854|gb|AW201125.1|AW201125EST: ATAAGCATCTTGTACGCCTTCTTGGATATTGTGTAGAANGGAGT-CATAG GCTGGCT-GTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTAC
genomic: ATAAGCATCTTGTACGCCTTCTTGGATATTGTGTAGAA-GGAGTTCATAGgtaaaaaaat ... tgatattcagGCTG-CTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtctctatatatgtattctgtcataatgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
gattgat putative branch site (score: 4)
tctatatatgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atattctactttgtccaaaattgaacataagcttttctctatgttatgtctctatatatgtattctgtcataatgaatgtgcttcccgattgatattcagGCTGCTTGTGTATGAATATGTGAACAATGGTAACTTAGAACAATGGTTACATGGAAACATGCACCAATATGGGACGCTTACCTGGGAGGCCCGCATGAAA
- - - - - - - ccaaaat
- - - - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgtc