Sequence
atgc intronic sequence ATGC exonic sequencegtacttcatcttaactgtacctattgaaactgaagatgataatatgctgattgttcatacttgaaaatcgacagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTCATGTGTATGATGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
Basic information
species | Glycine max |
transcript | GLYMA06G05900.1 |
intron # | 25 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 25
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 24
---------------------------------------------------------------------------------------------gtacttcatc--ttaactgtacctat-tgaaactgaagatgataatatgctgattgttcatacttgaaaatcg------acagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTCATGTGTATGATGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
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gtaatgcatctgcaaggagttttgctcaacaaatcaactcatttctctcctgccaagttcaatattaggatactatcttgtccagcaattattgtatttagtcaattgtttgtttttacctgataactgggttaatggtagagcaacactaaagcgctgtatatttgctgtcacagTGAGCAATGTTCCCCCCAAGCTGGTTATCCTTCATATGAACCTTTCCCTTCTTGTATACGAGGATATAATGACGATGACTGAAAACCTGAGTGAGAAGTA
upper sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
----------------------gtacttcat--cttaactgtacctattgaaactgaa--gatgataatatgctgattgttcatacttgaaa-atcgacagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTCATGTGTATGATGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
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attcaactcagtattttattttgtaagttataactggtcgctaatagttgatgctagaacggcattgatatcatg-ttgttgatattcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
upper sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 25
lower sequence: GRMZM2G463904_T03 (Zea mays), 3'ss of exon 24
--------------------------gtacttcatcttaactgtac--ctattga--aactgaagatgataatatgctgattgttcatacttgaaaatcgacagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTCATGTGTATGATGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
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cctgagttcagaattcaaatatgctgacaacttatgtgacttgtacggctgttaattaaataatattactaatgcactg-tgacagataaccttgcttcagCATCAAACAACATTCATCCCAAGCTTGTGATCCTCCACATGAACATGGCCCTCTATGTATATGATGATATAATGAGGATGACTGAAAACTTGAGCGAAAA---
upper sequence: GLYMA06G05900.1 (Glycine max), 3'ss of exon 25
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 24
-----------------------------gtacttcatcttaactgtacctattgaaactgaagatgataatatgctgattgttcatacttgaaaatcgacagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTCATGTGTATGATGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
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ttatatctgtatcccttaatatattttgaaaaatgtgttactattttcccttttgaaacttc---tctccatctactaactaatgtagtttgctaaacaacagTTACATACTCAACACCGAAGCTGGTGATCCTTCACATGAATATGGCACTGCATGTGTACGAGGATATCATGAGAATGACGGAAAACTTGAGTGAGAAGTAMapped 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|193541963|gb|FK496145.1|FK496145EST: CCGACCACACAATCCAACTTCTTTCGCTGATGGATCTTTTGACAAACCAG TCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTC
genomic: CCGACCACACAATCCAACTTCTTTCGCTGATGGATCTTTTGACAAACCAGgtacttcatc ... aaatcgacagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctattgaaactgaagatgataatatgctgattgttcatacttgaaaatcgacagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTCATGTGTATGATGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
tgctgat putative branch site (score: 3)
atgataatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacttcatcttaactgtacctattgaaactgaagatgataatatgctgattgttcatacttgaaaatcgacagTCAATTACTCACCTCCGAAGCTAGTGATTCTTCACATTAATATGACACTTCATGTGTATGATGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT