Sequence
atgc intronic sequence ATGC exonic sequence...aatttattgttatactggacatgaaaattaaacttaagtgattaatgatgaatggatgaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
Basic information
species | Glycine max |
transcript | GLYMA08G11240.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G11240.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g28420.1 (Oryza sativa), 3'ss of exon 2
-----aatttattgttatactggacatgaaaattaaacttaagtgattaatgatgaatggat-gaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
|| | | | | | || | || ||| | || || || |||| | | | | |||| | | ||||||| | ||||||||||| |||||||| |||||||| || |||||||| || ||| | || | ||||| | || || || | || || || ||| | ||
gtgcggatcggattcccagtttccccccacatttcgtcgcaat--attcaccatagttgaattgaattgccgaatcgtactgaatttttttgaaaaatc--tgcagGGGAGGTGATCAAGGGGTGGGATGAGGGTATCAAGACGATGAAGAAGGGGGAGCAGGCGGTGTTCACCGTTCCGCCGGAGCTCGCCTACGGCGAGGCCGG
upper sequence: GLYMA08G11240.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g28980.1 (Oryza sativa), 3'ss of exon 2
aatttattgttatactggacatgaaaattaaacttaagtgattaatgatgaatggatgaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
||| | |||| | | | || | | | | | | |||| | | | ||| ||| | | |||| ||||| || |||||||||||| || || || ||||||||||||||||||||||| ||||||| || || ||||| | || ||||| ||| ||
gcaatataaccaccaacaacatcatataattatgagaggagggagtatttagcaaacagtatattataaggtaaatgatgatgttactctctaattacagGCCAAGTTATTAAGGGATGGGATTTGGGCATTAAGACCATGAAGAAAGGTGAGAATGCTATTTTCACCATTCCACCAGAGCTTGCATATGGTGAGGATGG
upper sequence: GLYMA08G11240.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g41390.2 (Oryza sativa), 3'ss of exon 2
----aatttattgttatactggacatgaaaattaaacttaagtgattaatgatgaatggatgaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
| || || || | | || | | | | || | | || || | | || | ||| ||||| || |||| |||||||| || || |||||| ||||||||| |||||||||||||| || ||||| ||||||| || || || || ||||| ||||| || || ||
cacaagcttttttttctctgctatgtgcttgtgatggtgggattgcaaaatctatttttctgttaaatgctcaccagctatttcttg-aacttgt---atccagGTCAAGTGATAAAAGGTTGGGATCTAGGTATCAAGACCATGAAGAAAGGCGAAAATGCTGTTTTCACCATTCCTCCTGATTTGGCCTATGGTGAATCTGG
upper sequence: GLYMA08G11240.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G096585_T05 (Zea mays), 3'ss of exon 2
aatttattgttatactggacatgaaaattaaacttaagtgattaat-gatga-atggatgaat--aactatagtattcaatgttttgtgacttgactaatgc--agGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
| | | || |||| || | | || || | | | ||| || | | | || ||| | ||| | | | || ||||| ||| |||||||| ||||| |||||| |||| ||||| |||||||||||||| || ||||| |||| || || || ||||| |||||||||||| || ||
--gtaaattctagcttggagatcatcctgtttctctcttgcctctttgttgacattgccaagttgaaaaataatgctcattaact----attttgtcaatgcccagGTCAAGTGATAAAGGGTTGGGATCAAGGAATCAAGACCATGAAGAAAGGAGAAAATGCTATTTTTACCATTCCTCCAGAGCTGGCTTATGGAGCATCTGG
upper sequence: GLYMA08G11240.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ06798 (Selaginella moellendorffii), 3'ss of exon 2
aatttattgttatactggacatgaaaattaaacttaagtgattaatgatgaatggatgaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
| | || |||||| || || || || | | || | | || || ||| ||||| |||||||||||||| ||||| || || || |||||||| |||||||| || | ||||| || ||||| | |||||||||||||| | ||
----------------------------------------gtgagcgagttatggatttctatctg--gtgttgatttttctttcttcgtgcttgtgtagGCCAAGTTATCAAGGGATGGGACGAAGGCATTAAGACAATGAAGAAGGGTGAGAACGCGGTGTTCACCATTCCCCCGGCCTTGGCTTATGGAGAAGCTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgaatggatgaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
gactaat putative branch site (score: 2)
aataactatagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttattgttatactggacatgaaaattaaacttaagtgattaatgatgaatggatgaataactatagtattcaatgttttgtgacttgactaatgcagGGCAAGTGATCAAGGGATGGGATGAAGGTATCAAAACCATGAAGAAAGGTGAGAATGCCCTTTTCACAATACCCCCAGAATTGGCTTATGGAGAGTCAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - -atactgg
- - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - tgaatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacttg