Sequence
atgc intronic sequence ATGC exonic sequence...aacaactaattttcttcttttttccaaattattttttgtggtcctttttataagaaaaagttatattcgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
Basic information
| species | Glycine max |
| transcript | GLYMA19G24540.1 |
| intron # | 1 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g03350.1 (Oryza sativa), 3'ss of exon 2
aacaactaattttcttcttttttccaaattattttttgtggtcctttttataagaaaaagttatattcgtatg-ttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| | | | | || | || || | | | || || | ||| | | | | || ||| | || |||||| ||||| | | | | || | |||||||||| ||||| |||||||| |||||||| |||||||||||||| |||||| | || ||||| ||||
----gtcagtcctactatcttcttcatcttcatctgaacgaagaacacacgaacgaaccaagaaattaatctaactgaattcttgaatttttg-----cagGGGACCTGGCATCGCGGTGCTGATCCTGTCATGGATCATCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGGAAGCGGTTC
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G149216_T01 (Zea mays), 3'ss of exon 2
aacaactaattttcttcttttttccaaattattttttg-tggtcctttttataagaaaa-agttatattcgtatgttaattttgtgatctcctgtgt-tacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| | | || | | || | || | | | || ||| | | | | || | | | | ||| | ||| ||||||| ||||| | | | | | | |||| ||||||||||| || ||||| || ||||| |||||||||||||| |||||| | |||||||| ||||
--tgattcaattg-tacgagcgattaactcgttgtcagataaagattattagggggtcacgggcagataaatggttcattgttgattattggcgtgcacacagGGGCCCTGGCATCGCGGTGATGATCCTGTCGTGGATAATCACCCTATACACGCTATGGCAGATGGTGGAGATGCACGAGATGGTGCCTGGGAAGCGGTTC
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G127338_T02 (Zea mays), 3'ss of exon 1
aacaactaattttcttcttttttccaaattattt-tttgtggtcctttttataagaaaaagttatattcgtatgt-taattttgtgatctcc-tgtgt-tacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| || || | | | | | |||| | | || | | | | |||| | || | || | | || | | |||||| || || | | | | || || |||| ||||| ||||| || ||||| |||||||| |||||||||||||| |||||| |||| || || | ||
-------gtgcgtacgctagcttgctagctgtgtgcctgtgtctgactgactctgagcgcgcttaaattagatgtatcatatcatgccatgcatgcatatgcagGGGCCCCGGCATCGCGGTGCTGCTGCTGTCGTGGATCATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTCCCGGGCAAGCGCTTC
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G180659_T02 (Zea mays), 3'ss of exon 3
-------aacaactaattttcttcttttttccaaattattttttgtggtcctttttataagaaaaagttatattcgtatgttaattttgtgatctc--------ctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| | | | | | | | | | |||| | | | || | || || || ||| | |||||| ||||| | | | | || ||| |||| ||| | ||||| || ||||| |||||||| |||||||||||||| |||||| |||| ||||| ||||
gtacgtacgtgtccgagccatggatggatgctggagagagctcggctggtacatatatatagtcgtctgacgaccctaccccatccccgtcatgtcatgtcgatctgcactgcagGGGCCCTGGCATCGCGGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTCCCCGGGAAGCGGTTC
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G127294_T01 (Zea mays), 3'ss of exon 2
--------aacaactaattt-tcttcttttttccaaattattttttg--tggtcctttttataagaaaaagttat--attcgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| | | | | ||| | || | || | | | ||| | | | | | | || || | | ||| | | || | || ||||| || || | | || || ||| ||| ||||| |||||||| |||||||| |||||||||||||| ||| |||| ||||| ||||
gtccgtccgtcgtccgactcgtgctctactaatcacaccatcgatcgatcgatccatcagccatcatccatctgtcgatccggttctcaatctcgacggatc--gccttgcagGGAGGTCGGCGTCACGGTGCTGGTTCTGTTGTGGGCCATCACGCTCTACACGCTGTGGCAGATGGTGGAGATGCACGAGTGCGTCCCGGGGAAGCGGTTC
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G046743_T01 (Zea mays), 3'ss of exon 2
aacaactaattttcttcttttttc-caaattattttttgtggtcctttttataagaaaaagttatattcgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| | | | || | | ||| || | | | || | || || | || || ||| || || | | | | |||||| ||||| | | | || ||| |||| ||| | ||||| || ||||| |||||||| |||||||||||||| |||||| | || || || ||||
-gtacgcacacggcacatcttcgcgcgcgttacggttacggcgaccacaaacaaaatgaacttttttttgt-tgtcaa-------atggcatatat-gcagGGGCCCTGGCATCGCCGTGCTGGTGGTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCCGGAAAGCGGTTC
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G127328_T01 (Zea mays), 3'ss of exon 2
aacaactaattttcttcttttttccaaattattttttgtggtcctttttataagaaaaagttatattcgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| | | ||| | | | | | || | || | | | || | || | ||| | | | | | ||||||| | || | ||| | | |||| ||| | ||||| || ||||| |||||||| |||||||||||||| |||||| | || ||||| ||||
---------gtacgcacgcatcaatcaatcagtcatcatttccattctgatgataggag----tacttgt-catgaatgtaactactgctgtggattcagGGGTGCCGGCATCACGATCATGCTCCTGTCGTGGGTGATCACGCTGTACACGCTGTGGCAGATGGTGGAGATGCACGAGATGGTGCCGGGGAAGCGGTTC
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_71V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------aacaactaattttcttcttttttccaaattattttttgtggtcctttttataagaaaaagttatattcgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
||| | | || | | || |||| | || || | | || | | || | | | | | | | | | || ||| || |||||||| ||| | | || || | | |||||| | ||||| |||| |||||| |||||||||||||||||||| || | || || || | ||
gtatcaaccactacaccacagccagttcacgt-ttccttcctattttccttccgccattgttcccttctccacaaactttg-----aggatgacgtgg--gtatcatgt-ttgtagGGGTCCAGGTCTCCTAATGCTCATCCTTTCATGGGTCATCACCCTCTTCACACTCTGGCAAATGGTGGAGATGCACGAAGCTGTGCCCGGAAAGCGATTC
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 2
aacaactaattttcttcttttttccaaattattttttgtggtcctttttataagaaaaagtt-----atattcgtatgttaattttgtgatctcctgt--gttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| | | | | | | || | | | || | | ||| ||| | || | | | ||| ||| | | | ||| |||||| || || || | ||||||| |||| ||| | |||||||||||||| ||||||||||||||||| ||||| || ||| |||| ||||| || |||
-------accctagtcgtgtgtcgcccgcaatcctccagctccatgttcttgacaaatggttttccaacttttccaagcaactttaaagatttttttttcgttccagGGGACCGGGGGTCCTTGTTCTTGTACTGTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ25874 (Selaginella moellendorffii), 3'ss of exon 2
aacaactaattttcttcttttttccaaattattttttgtggtcc--tttttataagaaaaagtt-----atattcgtatgttaattttgtgatctcctgt--gttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| || | ||| | | ||| | || | || | | ||| ||| | || | | | ||| ||| | | | ||| |||||| || || || || ||||||| | || ||| | |||||||||||||| ||||||||||||||||| ||||| || ||| |||| ||||| || |||
---------gtgtcacccgcaatcctcaagaactttcacagccccatgttcttgacaaatcgttttccaacttttccaagcaactttaaagatttgtttttcgttccagGGGACCAGGGGTCCTGGTTCTTGTACTCTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT
upper sequence: GLYMA19G24540.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ10949 (Selaginella moellendorffii), 3'ss of exon 1
aacaactaattttcttcttttttccaaattattttttgtggtcctttttataagaaaaagttatatt-cgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
| | || |||||| || || ||| | | ||| | | || |||||| ||||| | | | || | | || |||| |||| |||||||| || |||||||||||||||||||| |||||| | || || | ||
----------------------------------------------gtaacgttcgaatgttataacgtctacattt-tttagggttcttcgtttttccagGGGGCCTGGGATCTTCGTGCTCCTCCTCTCCTGGACCGTCACGCTCTACACGCTATGGCAAATGGTGGAGATGCACGAGATGGTGGAGGGCAAGCGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttataagaaaaagttatattcgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
tgttaat putative branch site (score: 3)
tctcctgt putative PPT
aaaaagttatattcgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacaactaattttcttcttttttccaaattattttttgtggtcctttttataagaaaaagttatattcgtatgttaattttgtgatctcctgtgttacagGGGTCCTGGTGTGGTGATTCTTGTGTTGTCATGGATAATCACACTCTACACACTGTGGCAAATGGTGGAGATGCATGAGATGATCCCTGGGAAAAGGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - -ccaaatt
- - - - - - - - - - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
