Sequence
atgc intronic sequence ATGC exonic sequence...atcacactgtgcattccttctccagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgtacctttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
Basic information
species | Glycine max |
transcript | GLYMA07G02290.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 11
---atcacactgtgcattccttctc-cagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgtacctttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
| | |||| || |||| ||| | || || | |||| | | || || | | | | | || | | | |||| |||||||| |||| |||||||||||||||||| ||||||| ||||| |||||||||||||| ||||| || ||| |||| |||
tgaactttaatgtgtatgaagtctcatagtcaactcatatccaaatcgatcaattaca--gacatggttttttgttgat--ataattttttgttctcttcttagCTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 11
---------------------------atcacactgtgcattccttctccagtgcatgtggatattta------tggtgcaatgatattga-tattatgaggtaatcactgaagatatgtacct--ttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
|||| | || | | | || ||| | | | || ||| || | |||| | | | | || || | | | ||| | || | |||||||||||| ||||||||||||||||| ||||||||||||||||||||| ||||||||||||| |||||||| | ||||||
gtaaacttatgacttgaatgatctttgatcatagcgt-cgtaagtgcttcagatctttcgaatttttcgctctctgcttttctgatttaggctgctgagatatagcctttattgctattttccacatattttgcagCTTGCGTGGACATGTTATAACTTTTACCAATCAACTCCAACAAAACTGGCTGGGGAGAATTATTTCTTCAACTCTGGGAGT
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
lower sequence: AT1G51590.1 (Arabidopsis thaliana), 3'ss of exon 11
atcacactgtgcattccttctccagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgtacctttcttt---gcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
|||| | | || | || || ||| | | || || || || | | | | | ||| |||| ||||||||| ||||| ||||||||||| |||||||| || ||||| ||| | ||||| |||||||||||||| | | ||||||
------------------------gtgccttagaatctcaattgtatgttgagtataactttctgctgtg-tccttattgctgtttccctcactttactgcagCTTGCCTGGACTTGTTATAACTTTTACCAATCGACACCAACGAAACTTGCTGGAGAGAACTATTTCTTCACTGCAGGGCAG
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0054g00230.t01 (Vitis vinifera), 3'ss of exon 6
atcacactgtgcattccttctccagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgt---acct-ttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
| | | || | | | || || | ||| | || | | ||| ||| | || || ||| || |||||||||||| |||||||| ||||| |||||||| ||||| ||||||||||||||||| |||||||||||||| || |||||||||
----tgattccttctgccctccctgagttttctcttacttttccagcatttggatgcttttcatgtggttcctatgagtgaattgcttggcctattttttgcagCTTGCCTGGACATGCTATAATTTCTACCAGTCAACACCAACAAAATTGGCTGGAGAGAACTATTTCTTCCACTCTGGGCAG
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv09s0054g00370.t01 (Vitis vinifera), 3'ss of exon 11
------atcacactgtgcattccttctccagtgcatgtggatatttatggtgcaatg-atattgatattatgaggtaatcactgaagatatgtacctttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
| | | | | || || | | | | | || | ||| | || | | | |||||| ||| || |||| || |||||||||||| |||||||| ||||| |||||||| ||||| ||||||||||||||||| |||||||||||||| || |||||||||
tgattccttctgccctccctgagttttctcttacttttccaacatttggatgcttttcatgtggttcctatgagtgaattgcttgggata-------ttttttgcagCTTGCCTGGACATGCTATAATTTCTACCAGTCAACACCAACAAAATTGGCTGGAGAGAACTATTTCTTCCACTCTGGGCAG
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ33013 (Selaginella moellendorffii), 3'ss of exon 10
atcacactgtgcattccttctccagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgtacctttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
|| | | | || | | | ||| | | |||| | | | | ||||||| ||| ||||||||||||||||||||| || || ||||| | ||||| ||||| ||| ||| |||||| |||
-------------------------------------------gtactacctggtgaattctctaaagta--cgatatagatcggcatgtct---tgcagCTAGCTCGGACATGTTATAACTTCTACCGTTCTACACCAACTGGTCTTGCTGGCGAGAATTATAACTTCATTTCTGGCCAG
upper sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ30328 (Selaginella moellendorffii), 3'ss of exon 10
atcacactgtgcattccttctccagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgtacctttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
|| | | || | | | ||| | | |||| | | | | ||||||| ||| ||||||||||||||||||||| || || ||||| | ||||| ||||| ||| ||| ||||| |||
-------------------------------------------gtagtacctggtgaattctctaaagta--cgatatagatcggcatgtct---tgcagCTAGCTCGGACATGTTATAACTTCTACCGTTCTACACCAACTGGTCTTGCTGGCGAGAATTATAACTTCATATCTGGCCAGMapped 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|7924044|gb|AW830052.1|AW830052EST: GTTACAGTGCTGATGATGATTCACAGAAGTTTCTGTCACTTGCAGAAGAG CTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCT
genomic: GTTACAGTGCTGATGATGATTCACAGAAGTTTCTGTCACTTGCAGAAGAGgtatattttg ... ttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaatgatattgatattatgaggtaatcactgaagatatgtacctttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
tattgat putative branch site (score: 3)
tacctttcttt putative PPT
atattgatattatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atcacactgtgcattccttctccagtgcatgtggatatttatggtgcaatgatattgatattatgaggtaatcactgaagatatgtacctttctttgcagCTTGCTTGGACATGTTATAACTTCTACCAATCAACTCCAACAAAATTGGCTGGGGAGAACTATTTCTTTCATTCTGGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
atcacac
- - - - -tgcattc
- - - - - - - - cttctcc
- - - - - - - - - - - - -tgcatgt
- - - - - - - - - - - - - - - - - - - - -tggtgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtac