Sequence
atgc intronic sequence ATGC exonic sequence...taagtatgctttctggtgatatgctgttaaataggttagctttatgtgcttattactaaggagcataattattaacacatcacctatttgaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
Basic information
species | Glycine max |
transcript | GLYMA03G41050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g32960.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------taagtatgctttctggtgata-tgctgttaaataggttagctttatgtgct-tattactaaggagcataattattaac-------------acatcacctattt----gaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
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gtcagctctccaatttctgctctaggaacccaagttcttcgtttgtctcggtggtcaaatttgtttttccttgcacactctctttatctttaatcttctcagttctccctacaatggatgtaatatgatgaaaaaacatgatcccccatcgtgcttcgcttaatgttctctatctcgtgatcttatctagATGATGGAATGGTGGTATCAATCTGCTGAGGAAAGAATGTCAGCTCCGACTGTATATCCCCCACCCCCTCCTCCACCTCTGCCAAAG
upper sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G023970_T02 (Zea mays), 3'ss of exon 6
taagtatgctttctggtgatatgctgttaaataggttagctttatgtgcttattactaaggagcataattattaaca-catcacctatttgaa----ttatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
||| ||| | || | | | || | | | | || | | || || | | || | || | ||| |||| |||||||||| |||||||| || ||||| || || |||||||||||||| || |||||||| |||||||||||||||||| | || |||
---ctattagctctatccctgtggtagatatcatgtga--tatgaaccacgaatagtcgacaacacaactgtactcagtgttctctttctgataactttatccagATGATGGAGTGGTGGTATCAATCTGCTGAAGAAAGAATGTCAGCTCCGACTGTATATCCACCACCCCCTCCTCCTCCAACTCCTAAG
upper sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G04460.1 (Arabidopsis thaliana), 3'ss of exon 7
taagtatgctttctggtgatatgctgttaaataggttagctttatgtgcttattactaag--gagcataattat-taacacatcaccta----tttgaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
|| ||| | | || | ||| || || || | || | | || || | ||| || || | ||| | ||| || |||||||||||||||||||||| || || || || |||||| | |||||||| ||||| || |||||||| || ||||||||| | ||||||
-----atacttatggcgtttttgactctcggtagatt--tttcatcgcataatcatttagttgaacctaaacatctagctcattttcgtgtgtttttggttttgtagATGATGGAATGGTGGTATCAATCCGCTGAAGAGAGATTATCAGCTCCAACAGTGTACCCTCCACCTCCACCTCCTCCAGCCCCAAAG
upper sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0036g01130.t01 (Vitis vinifera), 3'ss of exon 7
taagtatgctttctggt---gatatgctgttaaataggttagctttatgtgcttattactaaggagcataattattaacacatcacctatttgaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
| ||| || | | | || | | | | | | || | || || | | | ||| ||| | ||||||| || |||||||||| ||||||||||| ||||| ||||| |||||||||||||| || ||||| || ||||| ||||| |||||||| ||||||
ttgacatgagttataatcatggtaggattctgttcttgct-gtttaacatgttt--tgtagatctagttttccattgacatgctattgatttgaactactcagATGATGGAGTGGTGGTACCAATCTGCTGAGGAAAGAATGTCAGCTCCAACTGTATACCCCCCACCACCTCCCCCTCCACCTCCAAAG
upper sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
lower sequence: PP1S26_47V6.1 (Physcomitrella patens), 3'ss of exon 7
taagtatgctttctggtgatatgctgttaaataggttag-ctttatgtgcttattactaaggagcataattattaacacatcacctatttgaa------------ttatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
||||| || | ||| | | ||| ||| | | || | ||| | || | | || | || | || | ||||| |||||||||||||||||||||| || || ||| || |||| ||| | || |||||||||||||||||||| || || ||| |
------------ttggtggcattttagcctatatctccgtcttcatgcgtcc-tagctgttgcacatgcatgttgaactgtggactttgtggaaactggaatcgtttgtacagATGGTGGAATGGTGGTACCAGTCTGCAGAAGAAAGAGTGACAGCACCTGCTGTTTATCCTCCACCCCCTCCTCCGCCGCCTCCAGTG
upper sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ15566 (Selaginella moellendorffii), 3'ss of exon 7
taagtatgctttctggtgatatgctgttaaataggttagctttatgtgcttattactaaggagcataattattaacacatcacctatttgaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
|| | || | | | | || | ||| | |||| | | ||||||||||||||||||| || ||||||||||| || | || ||||| ||||||| || || || || || || |||||||||
-----------------------------------------gtacgcactcttctttcac---tgcagttcc--atacaactcctaacacgagcct-cagATGATGGAATGGTGGTATCAATCTGCCGAGGAACGAGTCATGGCCCCTACGATATATCCCCCGCCTCCACCACCACCGCCACCAAAG
upper sequence: GLYMA03G41050.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ38878 (Selaginella moellendorffii), 3'ss of exon 7
taagtatgctttctggtgatatgctgttaaataggttagctttatgtgcttattactaaggagcataattattaacacatcacctatttgaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
| || | || | | || | ||| | |||| | | ||||||||||||||||||| || ||||||||||| || | || ||||| ||||||| || || || || || || |||||||||
-------------------------------------------gtacgcactctccttcc-actgcagttcc--atacaactcctaacacgagcct-cagATGATGGAATGGTGGTATCAATCTGCCGAGGAACGAGTCATGGCCCCTACGATATATCCCCCGCCTCCACCACCACCGCCACCAAAGMapped 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|11687819|gb|BF595495.1|BF595495EST: TACTTGACTATGCACAAACCGGATTGATTGCAGCAGTGTTCTTTTTTAAA ATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACA
genomic: TACTTGACTATGCACAAACCGGATTGATTGCAGCAGTGTTCTTTTTTAAAgtgagatggc ... aattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACA
EST:
gi|208337537|gb|GE136403.1|GE136403EST: TACTTGACTATGCACAAACCGGATTGATTGCAGCAGTG-TCTTTTTTAAA ATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACA
genomic: TACTTGACTATGCACAAACCGGATTGATTGCAGCAGTGTTCTTTTTTAAAgtgagatggc ... aattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgcttattactaaggagcataattattaacacatcacctatttgaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
tattaac putative branch site (score: 1)
ataattattaacacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taagtatgctttctggtgatatgctgttaaataggttagctttatgtgcttattactaaggagcataattattaacacatcacctatttgaattatgtagATGATGGAATGGTGGTACCAGTCTGCCGAGGAGAGAATGTCAGCTCCTACAGTATATCCTCCACCCCCTCCTCCTCCACCACCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- -gtatgct
- - - - - -tctggtg
- - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacacat