Sequence
atgc intronic sequence ATGC exonic sequencegtataatccaacaaatataacagccttagtgatgtaattgtttgggcaatgagattaagtgtctatgctatgtaatagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATG
Basic information
species | Glycine max |
transcript | GLYMA13G00420.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os04g51610.3 (Oryza sativa), 3'ss of exon 24
----------------gtataatccaa--caaatataa--cagccttagtgatgtaatt--gtttgggcaatgagattaagtgtctatgctatgtaatagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATG
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tgcattcaagtgcctagtttataccaggtcggtttttgttcagtatatgttgtctatcttcacctcgacaattaaatataccctatgtaaatggttacagGTGATGGGGAGGTCTTCACCAAATGACAAGCTTTTACTTGTTAAAGCATTAAGAAAAAGAGGTCATGTTGTTGCTGTGACTGGAGATGGCACAAATGATG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G140328_T03 (Zea mays), 3'ss of exon 24
------------------------gtataatcca--acaaatataacagccttagtgatgtaattgtttgggcaatgagattaagtgtctatgctatgtaatagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATG
|| | || || ||||| | || | | | |||||| | | ||| | | | | | |||| ||||| |||| || || ||||| || ||||| ||||| | ||| ||||| | || |||||||| ||||| ||||||||||| ||||||||||
aagttcttatataaatcttcatttgttttatgcattgcaaatgcagatatactatctacttttatctttggg---ttaatttatgctctaacaatg-gctacagGTGATGGGGAGGTCTTCACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCATGTTGTTGCTGTTACTGGAGATGGCACAAATGATG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 26
gtataatc-caacaaat-ataacag-ccttagtgatgtaat--tgtttgggca-atgagattaagtgt----ctatgctatg----taatagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATG
|||| ||| ||| |||| || || ||||| | | ||| || | || | | | ||| || || || || | |||||| |||||| |||| ||||| |||||||||||| | |||||||||||||||| | ||| ||||||||||| |||||||||||||||||||| |||||||
gtatgatctcaagaaatcatgtcattccttaattgtagaatattggctccacataccacactaattgaagtgctgtgtgattatatttatagGTCATGGGAAGGTCTTCTCCAAATGACAAGCTTCTTCTTGTGCAAGCATTGAAAAAGAAAGGGCATGTTGTTGCTGTAACTGGAGATGGAACTAATGATG
upper sequence: GLYMA13G00420.1 (Glycine max), 3'ss of exon 24
lower sequence: PP1S290_16V6.1 (Physcomitrella patens), 3'ss of exon 2
gtataatccaacaaatataacagccttagtgatgtaattgtttgggcaatgagattaagtgtctatgctatgtaatagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGG---AGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATG----------------------
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--ctagtagta-gagggtcgggactttcgcaattgggatgacagaaggctagccagcacagacttggataacctggtggtaatggcaaggtcctcaccactagACAAGCTGAAGCTTGTGAAAGCTTTGAAGGAGAGAAGAGGAGACGTCGTAGCGGTAACTGGAGATGGAACAAATGATGCTCCAGCGCTGAAAGAAGCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttagtgatgtaattgtttgggcaatgagattaagtgtctatgctatgtaatagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATG
taattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataatccaacaaatataacagccttagtgatgtaattgtttgggcaatgagattaagtgtctatgctatgtaatagGTTATGGGACGGTCATCTCCTAATGACAAGCTTTTGCTTGTGCAAGCATTGAGGAGGAAGGGGCATGTTGTGGCTGTAACTGGAGATGGAACAAATGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA