Sequence
atgc intronic sequence ATGC exonic sequencegtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
Basic information
| species | Glycine max |
| transcript | GLYMA18G51690.1 |
| intron # | 4 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
gtatgctatacaaaatgatgatgacaatgaaa-atgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
| |||| | | | | ||| | | | ||||| | | | || | | | |||| | | | || | ||| | |||| ||||||||| ||||| ||||| || || ||||||||||||||||||||||| || |||||| | || ||||||||| ||||||| |||||||||||||
----------------------ggcaatagcttacgttctgcatgcggcttgtcaactttggacatt-gtacattatccaatttgaaataaatcaatattgtgccctc--atcccttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC
upper sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g01240.2 (Oryza sativa), 3'ss of exon 13
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgat--gcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
| |||| ||| ||| | | | | | | | || | | | ||| |||| | | || | ||||| |||| || ||||| |||||||||||||||||||| ||||| || ||||| || || ||||| || || || ||||| | ||| | |||||||| || |
--------------------------ttaaaaagtatttctgccctgtagagtactgccagttttcccctggcattttctaattgaaagtatgcataggattaattggacttgacatttgctgcagACATTTAATGGCAAGAAATGGGAGAAATTCAATAGTGAAAAGGTGGCGTCGCTCGCATACGCCCGGATTCAAGGAAGGAGTGCTTTGATTGCTCATTTTC
upper sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
------------------------gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttata-atcacataacattcaca----gacacac------gcatacacactgtactaatagactaacttatgatg-catttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
||||| | ||||| | ||| | || | |||||||| | | ||| | || | | || | ||| | | || || | || || ||| | | ||| || ||||| || || |||||||| || ||||||||||| ||||||||||| || |||||| | || ||||||||| ||||||| |||||||| ||||
gtcagaaaattattccaattgacgaagtgctac-tgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
upper sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G451716_T01 (Zea mays), 3'ss of exon 13
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacata-aca-ttcacagacacacgcatacacactgtactaatagactaacttatgatgc--atttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
|| || || | |||| | | ||| || |||| | | | | | | | || ||| | | ||| | | ||| |||| || ||||||| | ||||||||||||||||||||||||||||| ||||| || |||||| | || ||||| ||| ||||||| ||||||| ||||
----------------------------aaagattatgaaggctaaatcttcgaatgcatgcacgcttcataaatagaaatggaaggagtataaaaatgaagaactttaacacatctgtctcttgcagACATTTCATGGGAAAAGGTGGGAGAAATTCAACAGTGAGAAAGTGGCCTCACTTGCTTATGCTAGAATCCAAGGAAAATCAGCTCTAGTTGCTCATTTCC
upper sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G156956_T01 (Zea mays), 3'ss of exon 12
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
||||| | || || | | ||| | || |||| | | | | || | | | | | | |||| || || ||| | | | || ||| ||||| || |||||||||||||| ||||| |||||||||||||||||||| || || || | || || || | ||| | |||||||| ||||
gtatgttcct----gtgcccataccttgatacctgacagtaagggaaaatatatctagtttaactccagaattggatgtgagaagatta-acta------tagct---gatacttctgtg-cagACATTCAACGGCAAGAAATGGGAGAAGTTCAATAGTGAGAAAGTGGCATCACTTGCGTACGCCAGAATCCAGGGAAGGAACGCTTTGATTGCTCATTTCC
upper sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 3
------------------------------------------gtatg-ctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatc--acataacattca-cagacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
|||| |||| | | |||| ||| | ||| | || ||| || || | | | || || || | | ||| | || || | || | ||| || | || | ||| | ||| || ||||| || || |||||||| || ||||||||||| ||||||||||| || ||||| | || ||||||||| |||| || |||||||| ||||
gtgagaattattcaattaaataagtgctactgtatcgtgcagttatggctattttgacttttgat--caacttatatggct--tgccaaatttgtacttcgataaaatatccatctggaacatggatgtgtgctatcctga---gctattttttcat-cgttttt--cagAGTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCCAGAATCCAAGGGAAAACAGCCCTGATTGCTCATTTCC
upper sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatt--tctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
| | | | | ||| | | || || |||| ||||| | || | || | | ||| ||||||||| |||||||||||||| || ||||| ||||| |||||||| || || || || || || ||||| || || || || || || |||||||
----------------------------------------------gttctctgtgaaaaagagagaggagattttcctacg-acttggttctaa------aacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC
upper sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ29693 (Selaginella moellendorffii), 3'ss of exon 10
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
||||| | | || | || || | | ||| || ||| |||||||| ||||| ||||||||||||||||| ||||| || || || || || || ||||| |||||||| || | || ||| | || || ||||
------------------------------------------------------------------gtttgacaccgttgttttcttcgtgcgcatt--ctcattctcgat------cttacagACCTTCAATGGAAAGAAGTGGGAGAAATTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
gactaac putative branch site (score: 1)
catttct putative PPT
tactaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttataatcacataacattcacagacacacgcatacacactgtactaatagactaacttatgatgcatttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
