Sequence
atgc intronic sequence ATGC exonic sequence...tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatgtcgtaaacatgccattatttatttttggatagAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
Basic information
species | Glycine max |
transcript | GLYMA18G05480.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 7
--------------------------tataggttttacaatta-ttgttctttcaatgtttcc-ttcaatgagctgca-ttatgggttaat--caaatgtcgtaaacatgccattatttatttttggatagAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
| || || ||| ||| || || | | |||||| || || || | | |||| | | | ||||||| ||||| ||||| ||| | | | | | | ||||| || ||| | | |||||||||||||| || ||| | ||||||||||||||||| ||
gtaagtactattatcattagcacatttttattattcacatttagtttttttatttgtgtttctgtttaaggatttttagttatctgctgttgataaatgtcctaaac---tgattatgtatgtagGCAATTCAGGGCCTATGTTGTCCGTTGATACAATTGAGAAAATGATGGAAGATCCAGCCGTGCAGAAGATGGTTTACCC
upper sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 10
lower sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
-----tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatgtcgtaaacatgcc-attatttattt------ttggatagAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
||| | || | | | || | | || || | || | |||| || | | || | ||| |||| | ||| || | | | || || || || ||||| |||||||||||||| || |||||||| |||||||||||||| ||
tgtgttatgattcttttttcttatatgctcacgttattgtctctcttttccttattctaaatttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC
upper sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
----tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatgtcgtaaacatgccattatttatttttggata--gAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
|| || | || | | ||| | | || || | | ||||| | || || |||| | ||| |||| | | | ||| | ||||||| ||||||||| |||||||||||||||| || ||||||||||| ||||||||||||||
atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
upper sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S110_13V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------------------------------------------tataggttttacaattattgttctttcaatgtttccttcaatgagctgcatt-atgggttaatcaaatgtcgtaaacatgccattatttatttttggatagAAAAATCAGTCT--TGTCAGTG--GATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
| | | || | | | | | | ||| || ||||| | | | || |||| ||| | | ||| | ||| ||| || | | |||| || |||||||| |||||||||||||||||||| || ||||||||||||||
gtacggtttctcaattaatacgcttttgaattccctttaccttgtgtcttaaatttgtctgcgcactgtgttcatttgtgaatcctgaaagagagtttgaaacatgcaccgagagaattcgaggtaccttgtaaaatttctcaaatggatggggctgttcgttatggttaacag-
upper sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S159_2V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatgtcgtaaaca-tgccattatttatttttggatagAAAAATCAG----TCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
| || || | | ||| || || || || || || | | | ||| | | ||| || | | ||| | | |||| | ||| ||| |||| | || || |||||||| ||||||||||| |||||||| || ||||||||||| ||
accttaaattgggaaagagggtttaaattatttacttagagtagttc--attttctattgggagaatttcgtaatgattgggttgtttgttgttgtctctagCATGGAATTCTGCTGGAAAAGGAAAACAGACGGTCTTCACTGTTGACCAATTGGAGAAGATGATGGAGGATCCAACAGTTCAAAAGATGGTTTACCCMapped 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|18716747|gb|BM522900.1|BM522900EST: AGCCCCCTCTAACCAAGGTTTTGGTGATTTTCCTGGTTCTCAATCTACNN NNNNNTCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAA
genomic: AGCCCCCTCTAACCAAGGTTTTGGTGATTTTCCTGGTTCTCAATCTACAAgtaagtacta ... ttttggatagAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcattatgggttaatcaaatgtcgtaaacatgccattatttatttttggatagAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
ggttaat putative branch site (score: 4)
tttattttt putative PPT
attatttatttttgga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatgtcgtaaacatgccattatttatttttggatagAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - -tgtttcc
- - - - - - - - - - - - - - - - - - - caatgag
- - - - - - - - - - - - - - - - - - - - - - - tgcatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgcca