Sequence
atgc intronic sequence ATGC exonic sequencegtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 25
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcact-ctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
|| | || || | ||| || | ||| | | | || ||||| | |||| ||| | | || | | | |||||||||| | | |||||| || ||||||||||||||||||||||| |||||||| |||||||| |||||||| | ||||| | |||||||| ||||
----gtttgtttcttatggcagggccttcta-----ttggtctatcagttttgctctgtttcaaaattttgaactgtttaattattatttgt-acagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAAGCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 25
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcact-ctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
|| | || || | ||| || | ||| | | | ||| ||||| | |||| |||| | | | | | | |||||||||| | | |||||| || ||||||||||||||||||||||| |||||||| |||||||| |||||| | | ||||| | |||||||| ||||
----gtttgtttcttatggcagggccttcta-----ttggtctatcagttttgctccgtttcaaaattttgaactatttcattattctttgt-acagGCTGGTCAGTTGCATCTTGTGAAACCATACATGGTTGCAGTTCAGAGCAACAATGTCTCTGCTGTGAATGAATCTTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 2
-gtagcattaatactgtcaacaatttcatc--ttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt-------atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
|||||| | | ||||| | | ||| | | ||||||||| | ||| || || || | | ||| ||| | |||||||||| | | |||||| || ||||| |||||||||||||||||||||||||| |||||||| ||||||||| | || ||| | |||||||| ||||
gttagcatctgaatgaaaatttatttccttagcgcactttggatagaagccctgttttcaaattccttcccccaaaatctgacttgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCTGTGAATGAAGCCTTGAACGAACTTTATGTTGAAGAGG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G062042_T02 (Zea mays), 3'ss of exon 10
--gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
| | | || || | | || | | | | || |||| ||| | | | ||| | | | ||| || | |||||||||| | | |||||| || ||||| |||||||||||||||||||||||||| ||||| || ||||||||| | |||||| | ||||| || || |
agttgaaactgatgaaagaaatagccctgttttgcactgtgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 2
-gtagcattaatactgtcaacaatttcatc--ttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
|||||| | | | ||||| | | ||| | | | ||||||| ||| | | | | | | ||| || | |||||||||| | | |||||| || ||||| |||||||||||||||||||| ||||| |||||||| ||||||||| | ||||| | |||||||| ||||
gttagcatctgaatggaaatttatttccttagcgcactttgaatagaagccctgtttcaaattccttccaaaatcttactgtcttgttgctctttggacagGCTGGTCAATTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAATAATGTCTCTGCTGTGAATGAAGCCTTGAATGAGCTTTATGTTGAAGAGG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G091121_T01 (Zea mays), 3'ss of exon 5
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
| | ||| | | || |||| ||| || | | ||| | | | ||| || | |||||||||| | | |||||| || ||||| |||||||||||||||||||||||||| ||||| || ||||||||| | |||||| | ||||| || || |
--------------------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCGTGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 24
-gtagcattaatactgtcaacaatttcatct-taatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
|||||| | | ||| | | | ||| | | || |||| ||| | | | ||| | | | ||| || | |||||||||| | | |||||| || ||||| |||||||||||||||||||||||||| ||||| || ||||||||| | ||||| | ||||| || ||||
gttagcatctgattgaaaatctattcctgcagtgcactttgaatagaagccctgtttcaattccgtcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTATCTGCCGTGAATGAAGCCTTGAATGAGCTTTATGTCGAAGAGG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G115138_T01 (Zea mays), 3'ss of exon 9
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
| | ||| | | || |||| ||| || | | ||| | | | ||| || | |||||||||| | | |||||| || ||||| |||||||||||||||||||||||||| ||||| | ||||||||| | |||||| | ||||| || || |
--------------------------gtagtgcactttgaatagaagccctatttcaattccatcccaaaaatctgattcttgttgctctttggacagGCTGGTCAGTTGCATCTTGTGAAACCATATATGGTTGCAGTTCAGAGTAACAATGTCTCTGCCATGAATGAAGCCTTGAATGAACTTTATGTCGAAGATG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 10
gtagcattaatactgtcaacaatttcatcttaatttttacttt----ataacctgttttccatttcactctatgaatattttccctgtgatgtatt--atagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG-----------------------------------------------------------------------
| | || | | ||| | | | | ||||| | || | | || || ||| | | ||| | | | ||| || | |||||||||| | | |||||| || ||||| ||||||||| |||||||||||||||| ||||| | |||| |||| | ||||| | ||||| ||||
---gtaagcatctgattgaaaatctatttctgcagtgcactttgaatagaagccctgtttcaattcctcccaaaaatctgattcttgttgctctttggacaggctggtcagttgcatcttgtgaaaccatatatggttgcaattcagagtaacaatgtctctgccatgaatggagccttgaatgagctttatgtctgagagGAGGACTATGAGAGACTCCGTGAATCAGTTGACACGCATGACAACTTTGACCAGATTGGTCTTGCCCAGAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 25
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
| || | | || | || ||| || | | ||| | |||| ||| | | | |||| |||| | |||||||||| | |||||| |||||||||||||| ||||||||||||| |||||||| |||||||||||||| || || ||||| ||||| || || || |
---gttagaagctgactgatgactttgtttt--tttctataaaaacaactgagctacatt--acttaacaattggtttcttc-tgatct----cagGCTGGTCACTTGCGTCTTATCAAGCCATACATGATTGCAGTTCAGAGCAACAATGTCTCTGCTGTTAATGAGGCTCTGAATGAGATATACGTGGAAGAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 25
---gtagcattaatactg--tcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatatt-ttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
|| | | | || | || | |||| | || ||| | | | | || || | | | | ||| ||| || | ||| || |||||||||| | || ||| | |||||||| ||||||||||||||||| || ||||| |||||||| |||||||| || ||||| ||||||| || || |
gttagaggctgaccattgatttaatattttctgttaaaaactta--tcaccagtggcttaacaatcta-tatctgatgattatttcttgtttctgatctcagGCTGGTCACTTGCGCCTTATTAAGCCATATATGGTTGCAGTTCAGAGCAATAATGTATCTGCTGTAAATGAAGCTCTGAATGAGATATATGCAGAAGAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 25
------------------------gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgt---tttccatttcactctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
|| | || | || || | || ||| || || | || | | | | || | | || ||| | || || ||| |||| ||||| || | |||||| |||||||| |||||||||||||||||||||||||| |||||||| ||||| || | |||| || |||||||||||||
gtttttgtttgtgctggcttttttgtttcctttcttct-tcttctgaagtatgttacttgtttccttgactcttctagacgtttatgtactcttttggttatgcgttttttgttggattccagGCAGGTCACCTTCATCTTGTGAAGCCATATATGGTTGCAGTTCAGAGTAACAATGTTTCTGCTGTGAATGAGGCTTTGAATGGGATTTATGTTGAGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttataacctgttttccatttcactctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
ttataac putative branch site (score: 2)
tctatgaatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagcattaatactgtcaacaatttcatcttaatttttactttataacctgttttccatttcactctatgaatattttccctgtgatgtattatagGCTGGTCATCTCCGTCTTGTCAAGCCATACATGGTTGCAGTTCAGAGTAACAATGTGTCTGCTGTTAATGAAGCCCTTAATGAAATATATGTTGAGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG