Sequence
atgc intronic sequence ATGC exonic sequence...gactttccttgaacgataatttccttaccatggttaaataatttttattactcacactacattttttattttattttctttccctaatttatgaatgcagTTCATCACATTTGGATTTGCGTGTACTCCGTTGTACTTCGTGTGGGAGAAGGTGATTGGGATGCACGACACAAAGAGCATTTGTTTGAGGGCACTTGCAC
Basic information
species | Glycine max |
transcript | GLYMA1403S00200.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA1403S00200.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g02030.t01 (Vitis vinifera), 3'ss of exon 7
----------gactttccttgaacg-at---aatttcctt--accatggttaaataatttttattactcacactacattttttattttattttctttccctaatttatgaatgc---agTTCATCACATTTGGATTTGCGTGTACTCCGTTGTACTTCGTGTGGGAGAAGGTGATTGGGATGCACGACACAAAGAGCATTTGTTTGAGGGCACTTGCAC
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gtttgtaaattaattcactcaagtgcattcaaattattttgaattattggtagacgtaatgactgacttggcctcaagatagtgaaacttttactgataaaaatgcatgggtgttgtagTTTATTACATTTGGGTTCGCATGTACGCCACTGTACTTCGTGTGGGAGAAGGTGATAGGGATGCATGACACAAGGAGCATCTGTTTAAGGGCACTGGCCA
upper sequence: GLYMA1403S00200.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S211_67V6.1 (Physcomitrella patens), 3'ss of exon 6
---------------------------gact-ttccttga------acgataatttccttaccat--ggttaaataatttttattactcacactacattttttattttatttt---ctttccctaatttatgaatgcagTTCATCACATTTGGATTTGCGTGTACTCCGTTGTACTTCGTGTGGGAGAAGGTGATTGGGATGCACGACACAAAGAGCATTTGTTTGAGGGCACT-TGCAC
||| ||| | || | |||| || | | | || | | ||| | || ||| || | | | | || | | ||||||||||||| |||| ||||| ||||| |||||||||||||||||||||||||| ||||| ||| |||| ||||| || ||||| || | |||
gtactcaaggcacccatcattctaaaaaactattcgtcgatgtgccatattaatcctctgaacgtcaggactgaagctacttactgtggacgaagcatcttctctgaagggtctaacgacattgaaaatcttgctgcagTTCATCACTGTTGGCTTTGCCGTCACTCCATTGTACTTCGTGTGGGAGAAGGTGATCGGGATTCACAACACGAAGAGTCTTCCCTTGAGAGCGGTATGCC-
upper sequence: GLYMA1403S00200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ18760 (Selaginella moellendorffii), 3'ss of exon 6
gactttccttgaacgataatttccttaccatggttaaataatttttattactcacactacattttttattttattttctttccctaatttatgaatgcagTTCATCACATTTGGATTTGCGTGTACTCCGTTGTACTTCGTGTGGGAGAAGGTGATTGGGATGCACGACACAAAGAGCATTTGTTTGAGGGCACTTGCAC
| || || | | || | | || || | | | | || | | | | |||||| || || ||||||||||| || || || ||||||||||||||||||||| | ||||| | || | || | | | ||| ||| |
-------------------------------gtaagaaagatcatcgatgatc-tatgatcttcgttcctggagctaaacttcccattgtct---cgcagTTTATTACGTTTGGATTTGCTTGCACGCCCTTGTACTTCGTGTGGGAGAAGATAATTGGCGTCCATAGAAGTCCAAGGTTCCTACTTCGAGCAGCTGCCC
upper sequence: GLYMA1403S00200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 6
-------------------------------------------------------------gactttccttgaacgataatttccttaccatggttaaataatttttattactcac--actacattttttattttattttctttccctaatttatgaatgcagTTCATCACATTTGGATTTGCGTGTACTCCGTTGTACTTCGTGTGGGAGAAGGTGATTGGGATGCACGACACAAAGAGCATTTGTTTGAGGGCACTTGCAC
||| | | | | ||| || | ||| || | | | | | | ||| | | ||| || ||| ||||||||||| |||||||| || || || ||| ||||| |||||||||||||| | | || || ||| | || | | || | || || ||
gtcattctcatgctcatccatcaggcaagcttttttctttcctcgagctcttctttacttcttcttcttcttcttcttcttcttcttcccgagaagaaagaaagaggaaagtttgccaagtttttctttcttctgattcctcgattctcgcgatggaaaacagTTCATCACGTTTGGATTCGCATGCACGCCGCTGTACATCGTGTGGGAGAAGATTCTGGGCATTCACAAGACGGCCAATCTCCCCGTGCGAGCGCTGGCCA
upper sequence: GLYMA1403S00200.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 6
------------------------------------------gactttccttgaacgataatt----tccttaccatggttaaataatttttattactcac--actacattttttattttattttctttccctaatttatgaatgcagTTCATCACATTTGGATTTGCGTGTACTCCGTTGTACTTCGTGTGGGAGAAGGTGATTGGGATGCACGACACAAAGAGCATTTGTTTGAGGGCACTTGCAC
|| | ||| | | || | ||| || | ||| || | | | | | | ||| | | ||| || ||| ||||||||||| |||||||| || || || ||| ||||| |||||||||||||| | | || || ||| | || | | || | || || ||
gttctcatgctcatccatcaggcaagcttttttctttcctcgagctcttctttacttcttcttcttcttcttcccgagaagaaagaaagaggaaagtttgccaagtttttctttcttctgattcctcgattctcgcgatggaaaacagTTCATCACGTTTGGATTCGCATGCACGCCGCTGTACATCGTGTGGGAGAAGATTCTGGGCATTCACAAGACGGCCAATCTCCCCGTGCGAGCGCTGGCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tattactcacactacattttttattttattttctttccctaatttatgaatgcagTTCATCACATTTGGATTTGCGTGTACTCCGTTGTACTTCGTGTGGGAGAAGGTGATTGGGATGCACGACACAAAGAGCATTTGTTTGAGGGCACTTGCAC
attttttattttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gactttccttgaacgataatttccttaccatggttaaataatttttattactcacactacattttttattttattttctttccctaatttatgaatgcagTTCATCACATTTGGATTTGCGTGTACTCCGTTGTACTTCGTGTGGGAGAAGGTGATTGGGATGCACGACACAAAGAGCATTTGTTTGAGGGCACTTGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - ccttgaa
- - - - - - - - - - - ccttacc
- - - - - - - - - - - - - - - - - - - - - - - - -actcaca