Sequence
atgc intronic sequence ATGC exonic sequence...tttctttcttatgataactgaatcaagtttaagccccccttttggattaacatgatattattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
Basic information
species | Glycine max |
transcript | GLYMA08G14240.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S422_18V6.1 (Physcomitrella patens), 3'ss of exon 3
tttctttcttatgata-actgaatcaagtt-taagccccccttttggattaacatg--atattattggcatcaaaacccc-ttgaaattgatttgtgtt--ttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
||||| | ||| | | | || ||||| ||| | | ||| || ||||| ||| | ||| || | || | |||||||||||| | ||||| || ||||| || || || ||||||||||| ||||| || || ||| | |||||||| |||||||||| ||||| |||||||
-------actatgacatactagtgtaggacattggcaagagttttgcatttatgagttgtataatgatcatcagaacgacgttgtccatgcccccttttcatcccagGTTGATTATTCCTGCACTCCGGAAGAGGTACAACAGCACTTTCAGTCATGTGGGACAGTGAACCGTGTCACTATTTTGACAGACAAATTTGGGCAGCCTA
upper sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S85_168V6.1 (Physcomitrella patens), 3'ss of exon 3
--tttctttcttatgataactgaatcaagtttaagccccccttttggattaacatgatattattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
| |||| | | || | || || | | || | | | | || ||| | | | | |||| ||| || || |||||||||||||| ||||| ||||||||||| || || || |||||||| |||||||| || || | ||||| || |||| ||||||||||| || |
gtacacgcaactatgttta-tgcagcagtttaaggtcctgcgtactttgtgaaggaattttagcgaacacttagtctgagtttattg-tttctgcttcgcagGTTGATTATGCCTGCACTCCAGAAGAAGTACAACAGCATTTTCAGTCGTGTGGTACAGTTAATCGTGTCACAATTTTGACTGACAAGTTTGGATCACCCA
upper sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S433_16V6.2 (Physcomitrella patens), 3'ss of exon 3
tttctttcttatgataactgaatcaagtttaagccccccttttggattaac--atgat-attattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
| || |||| | | | | | | | || | || || | ||| || || | | | | | ||| || | |||| |||||||||||| | ||||| || ||||| ||||| |||||||| ||||| ||||| || || ||| | ||||| || |||| ||||||||||| ||||| |
-tagttggatatgttg-caggagctcctgcatttatgagttgtagaatagttaacgatgatcatcagtgtgacgttgtccttttattctcttttctttt-cagGTTGATTATTCCTGCACTCCGGAAGAGGTGCAACAACACTTCCAGTCGTGTGGGACGGTGAACCGTGTCACAATTTTGACGGACAAGTTTGGGCAGCCCA
upper sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S3_616V6.1 (Physcomitrella patens), 3'ss of exon 3
tttctttcttatgataactgaatcaagtttaagccccccttttggattaaca------tgatattattggcatcaaaaccccttgaaattgatttgtgtttt---acagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
| | |||| ||| | | | |||||| || | || | || | | || || | | || ||| | ||| |||||||||||| | ||||| ||||||||||| || |||||||||||||| ||||| || || || | ||||| || |||| ||||||||||| ||||| |
--------tccaagtgactgtttcaggagctc-catctcttttgagctagtaaagcagcgacagaatcgtagtgaacacttgattgagtttattattttttctgcgcagGTTGATTATTCCTGCACTCCAGAAGAAGTACAACAACACTTTCAGTCATGTGGCACAGTGAATCGCGTCACAATTTTGACCGACAAGTTTGGACAGCCAA
upper sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ23874 (Selaginella moellendorffii), 3'ss of exon 3
tttctttcttatgataactgaatcaagtttaagccccccttttggattaacatgatattattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
|||| | | ||| || | | || || | ||| ||| || | ||| || |||| |||||| | ||||||||||| ||||| || ||||||||||| |||||||| ||||| ||| |||| ||||| || || |||||||| || ||||| |
----------------------------gtaagtcttcttttc---ttctcttctcgtt----gccttggaacttagtgag--tggtatgttctt---agGTGGATTATTCGTGCACACCAGAGGAAGTCCAACAACACTTTCAATCCTGTGGCACTGTTAACCGGGTTACTATTCTAACTGACAAGTTCGGACAGCCCA
upper sequence: GLYMA08G14240.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10007 (Selaginella moellendorffii), 3'ss of exon 2
tttctttcttatgataactgaatcaagtttaagccccccttttggattaacatgatattattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
|||| | ||| || | | || || | ||| ||| || | ||| || |||| |||||| | ||||||||||| ||||| || || |||||||| |||||||| ||||| ||| |||| ||||| | || |||||||| || ||||| |
----------------------------gtaagttttcttttc---ttctcttctcgtt----gccttggaacttagtgag--tggtatgttctt---agGTGGATTATTCGTGCACACCAGAGGAAGTCCAACAGCACTTTCAATCCTGTGGCACTGTTAACCGGGTTACTATTTTAACTGACAAGTTCGGACAGCCCAMapped 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|192334398|gb|FK024441.1|FK024441EST: CTCAGGCAAACAAGGAGGAGGCAGATGCTCGGTCTGTTTTTGTTGGCAAT GTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
genomic: CTCAGGCAAACAAGGAGGAGGCAGATGCTCGGTCTGTTTTTGTTGGCAATgtatgaatca ... tgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attaacatgatattattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
atgatattatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttctttcttatgataactgaatcaagtttaagccccccttttggattaacatgatattattggcatcaaaaccccttgaaattgatttgtgttttacagGTTGATTATGCATGCACACCAGAAGAAGTGCAGCAACACTTTCAGTCCTGTGGTACTGTAAACAGGGTCACTATCCTGACAGACAAGTTTGGCCAGCCTA
- - - - - - - - - - - - - - - - -cccccct
- - - - - - - - - - - - - - - - - - - - - - - - - catgata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatttg