Sequence
atgc intronic sequence ATGC exonic sequencegtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
Basic information
species | Glycine max |
transcript | GLYMA11G35460.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
|| || || || || ||| | || || | | || | |||||| | || |||| ||| | | || | | | |||||||||| | | |||||| || || |||||||||||||||||||| ||||| || |||||||| |||||||| ||||||| | |||||||| ||||
gtttgtttctta-tggcagggccttc-tattggtctatcagttttgctctgtttcaaaattt-----tgaactgtttaattattatttgt-acagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
|| || || || || ||| | || || | | || | | |||| | || |||| |||| | | | | | | |||||||||| | | |||||| || || |||||||||||||||||||| ||||| || |||||||| |||||| | ||||||| | |||||||| ||||
gtttgtttctta-tggcagggccttc-tattggtctatcagttttgctccgtttcaaaattt-----tgaactatttcattattctttgt-acagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 2
-gtagcattaatactgtcaacaatttcattttagtttttactttataa--cctgttttccatttcactgat---gaat---attttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
|||||| | | ||||| || | || || || ||||||||| | ||| | ||| | || | ||| || | |||||||||| | | |||||| || || || ||||||||||||||||||||||| || |||||||| ||||||||| |||| ||| | |||||||| ||||
gttagcatctgaatgaaaatttatttccttagcgcactttggatagaagccctgttttcaaattccttcccccaaaatctgacttgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCTGTGAATGAAGCCTTGAACGAACTTTATGTTGAAGAGG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
--gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttca-ctgatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
| | | || || | |||| | | | | || |||| ||| | | | ||| | | | ||| || | |||||||||| | | |||||| || || || ||||||||||||||||||||||| || ||||| || ||||||||| |||||||| | ||||| || || |
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
-gtagcattaatactgtcaacaatttcattttagt-ttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtatt----atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
|||||| | | | ||||| || | ||| | | || |||| | ||| | ||| || || || | | |||||||||| | | |||||| || || || |||||||||||||||||||| || || |||||||| ||||||||| ||||||| | |||||||| ||||
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttca-ctgatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
| | ||| | | || |||| ||| || | | ||| | | | ||| || | |||||||||| | | |||||| || || || ||||||||||||||||||||||| || ||||| || ||||||||| |||||||| | ||||| || || |
--------------------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
-gtagcattaatactgtcaacaatttc-attttagtttttactttataacctgttttccatttca-ctgatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
|||||| | | ||| | | ||| | | || |||| ||| | | | ||| | | | ||| || | |||||||||| | | |||||| || || || ||||||||||||||||||||||| || ||||| || ||||||||| ||||||| | ||||| || ||||
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 9
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttca-ctgatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
| | ||| | | || |||| ||| || | | ||| | | | ||| || | |||||||||| | | |||||| || || || ||||||||||||||||||||||| || ||||| | ||||||||| |||||||| | ||||| || || |
--------------------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCATGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
| || | | || |||| ||| || | | ||| | |||| ||| | ||| || | | |||| | |||||||||| | |||||| ||||||| |||||| ||||||||||||| ||||| || |||||||||||||| || |||||||| ||||| || || || |
---gttagaagctgactgatgactttgtttt--tttctataaaaacaactgagctacatt--acttaacaattggtttcttctgatct----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
---gtagcattaatactg--tcaacaatttcattttagtttttactttataacctgttttccatttca---ctgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
|| | | | || | || | |||| || | ||| | | | | || || | | ||||||| ||||| | ||| || |||||||||| | || ||| | ||||| || ||||||||||||||||| || || || |||||||| |||||||| |||||||| ||||||| || || |
gttagaggctgaccattgatttaatattttctgttaaaaactta--tcaccagtggcttaacaatctatatctgatgattattt--cttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
upper sequence: GLYMA11G35460.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
-------------gtagcattaatactgtcaacaatttcatttt--agttt-ttactttataacctg--ttttcca----ttt-----cactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
| || || | | | | | || | ||| | |||||| | | || | ||| | ||| | || || ||| | || || ||| |||| ||||| || | |||||| ||||| || ||||||||||||||||||||||| || |||||||| ||||| || |||||| || |||||||||||||
gtttttgtttgtgctggcttttttgtttcctttcttcttcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttataacctgttttccatttcactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
atgaatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcattaatactgtcaacaatttcattttagtttttactttataacctgttttccatttcactgatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCTTACATGGTTGCAGTTCAGAGTAACAACGTGTCTGCTGTTAATGAAGCCCTGAATGAAATATATGTTGAGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG