Sequence
atgc intronic sequence ATGC exonic sequencegtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcacctaataatttgagatgtggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
Basic information
species | Glycine max |
transcript | GLYMA12G35510.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G53165.2 (Arabidopsis thaliana), 3'ss of exon 7
gtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcacctaataatttgagatgtggacttgcatacatgtggaatgt-caccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
||| | | | || || | |||| ||| | || |||| | | ||| | ||| || | ||| | || | | | | | |||||||||| |||||||||||||| |||||||| |||||||||||||| |||||
----------------------gtattttctacttcttaaacttatttgattaatttcttaaat--tttcttttata-tccgagtggtttagttgga-acttctttcacgcatattagGTTGCAGACTTTGGTGTTTCTGCACAATTAACCCGGACTATATCAAGGCGAAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 7
----------------gtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcacctaataatttgagatgtggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
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gtaatccttgatgctcaaataatcctttgcaccaaatctaactcattggaagaatgctatacataatatggatgagcatgcgtgctcttctt--tctggtttctgaattt-tatgtttctgaccttgtaacagGTTGCAGATTTTGGCGTTTCTGCGCAATTAACAAGGACAATCTCAAGGAGGAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 5
gtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcacctaataatttgagatgtggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
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---attggtatcctaaaaaa---tacagctagtctgttggttttataa---ttcgtgtttttgtgatac-----gtgat--gaaataaatatcggctctgatgggaagtggtgc-agGTTGCAGATTTTGGAGTTTCTGCTCAGCTGACTCGTACAATGTCCAAACGCAAG
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 6
gtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcaccta-ataatttgagatgtgg-acttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
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-------------------------------------------------------------------gtaactgcgtggtttagaaggtcgtgattgtactcatattttataaaac-agGTTGCAGATTTTGGGGTTTCTGCTCAGCTCACACGTACTGTGTCCAAGCGGAAA
upper sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15774 (Selaginella moellendorffii), 3'ss of exon 6
gtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcaccta-ataatttgagatgtgg-acttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
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-------------------------------------------------------------------gtaactgcgtggtttagaaggttgtgattgtactcatattttataaaac-agGTTGCAGATTTTGGTGTTTCTGCTCAGCTCACACGTACTGTGTCCAAGCGGAAAMapped 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|11688820|gb|BF596496.1|BF596496EST: CTGCAAACATTTTATTGTCTGAGAATGGTGATGTAAAG GTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGA
genomic: CTGCAAACATTTTATTGTCTGAGAATGGTGATGTAAAGgtacgttata ... atgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGA
EST:
gi|9899540|gb|BE608508.1|BE608508EST: CTGCAAACATTTTATTGTCTGAGAATGGTGATGTAAAG GTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGA
genomic: CTGCAAACATTTTATTGTCTGAGAATGGTGATGTAAAGgtacgttata ... atgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgatgcacctaataatttgagatgtggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
acctaat putative branch site (score: 3)
taataatttgagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgttatattctgacagaggttatatacaatttgtttattttatatgacttcattgaaaaatgatgcacctaataatttgagatgtggacttgcatacatgtggaatgtcaccagGTTGCAGATTTTGGTGTTTCTGCTCAATTAACAAGGACTATATCAAGGAGAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA