Sequence
atgc intronic sequence ATGC exonic sequencegtaagcctttcttgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
Basic information
species | Glycine max |
transcript | GLYMA07G40210.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g66350.1 (Oryza sativa), 3'ss of exon 10
----------------------------------gtaagcctttcttgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctct---taaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
| || | | ||||| || ||||||| | | || | ||| | || | | | | | || || | | |||| |||||||| || ||||||||||||||| |||| | ||||| ||||| ||||||||||||| |||||||||||||||||| | ||||| || ||||
gtacatccttagttccttgaccaccagcacataaacacaaacccacagaagacattgcattttctgtttccctcttaaagagtgtcatttcattcactggtcggctatatctgggcatatgaaatatttccttcatatatctaacttacagGATGAGAGATACATGGTAACATATAACCCCGCAAAGGATAAGGTATATGCTTTGCTCAAGGATCAAGCAAAGTCAGATGACATTATCAAAGCGGCTTTCC
upper sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os05g34650.1 (Oryza sativa), 3'ss of exon 10
gtaagcctttcttgagagcttgagatttttca-gctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
|| ||| || ||| || || | | |||| | | | | | | | || |||| |||| | || | || || | || ||||| || ||||| ||||||||||| |||| ||||||| ||||| |||||||||| || |||||| ||||||| ||||| ||||| || ||||
---gtactatctcga-----tgatgttattagtatttgtccttagactgttcttttccttcattagcacaatagagcattggcatgtgtgaagttgtgatatattttaattgtagGATGAGAGGTACATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGATATTCTCAAAGCCGCTTTCC
upper sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G833124_T01 (Zea mays), 3'ss of exon 10
gtaagcctttcttgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
| | || || | |||| || | | ||| ||| | | | ||| |||| || |||||| | | ||| ||| ||||| |||||||| ||||||||||| |||| ||||||| ||||| |||||||||| || |||||| ||||||||||||| ||||| || || |
-----------------gtaccatcttatttgctccattctgaatgctttctttctttggtgtaatca-aggat-tgttct-gtg-aagttgcaa---cgtggtttggctgcagGATGAGAGGTATATTGTTACATATAACCCAACAAAGGACAAGGTATATGCTTTGCTCAAGGACCAAGCAAAGCCAGATGACATTCTCAAAGCTGCTTTTC
upper sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G081188_T03 (Zea mays), 3'ss of exon 2
------------------------------------------------gtaagcctttct-tgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
| || || | | | || | || | ||| | || ||| || | | ||| ||| | | ||| || | | || || || | | || |||||||| || |||||||||||||| |||| | || || ||||| |||||||||| |||||||| ||||| |||||| | ||||| || ||||
gtatgtcctctctggacaccagcaattaaaaaacaaatccagaaactactctgctttcatatatgtgcagtaatttctccagaaactactctggacaccagcttcatt-tcttgccatacaacctctgcttttggtatgaacat-ctggtatcttaattatagGACGAGAGATACATGGTAACATATAACCCAACAAAGGATAAAGTATATGCTTTGCTCAAGGACCAGGCAAAATCAGACGACATTATTAAAGCTGCTTTCC
upper sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagcctttcttgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
| | ||| || ||| || | | ||| | || || | | | ||||||| | | | |||| || ||||| || ||||| || | ||| | || || || ||||| ||||||| ||||||| || |||||||||||||| ||||||||||| |
-----------------------------gtatgtgttttttcccttaatatcaagccttgaccgctttatcttg-atactgtaattgactttattctcttta-ctaatggcagAAAGAAAGATACATGGTAACGTACAGCCCTACCAAGGGTAAAGTCTATGCACTGCTCAAACATCAGGCTAACTCAGATGACATTCTCAAAGCAGCATTTC
upper sequence: GLYMA07G40210.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 10
gtaagcctttcttgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgt---tctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
| | | ||| | || | | | | | || | |||||| | || | | |||| | |||||| || | ||| | ||||| ||||||||| | || |||||||| || || || || || |||||| | || ||||||||||||||||| ||||||||||| ||||| || ||||
-----------------gtgcgtgcacacacagagatggattgagtaatatcccctttaaatgtgttatttctgtcactttcatgtgaattgtgtatatcctctttgttggtgacagAAAGAGAGATATCTAGTGACATATAATCCTTCGAAGGGTAAAGTGTATGCGTTACTGAAGGATCAGGCAAAGTCTGATGACATTCTAAAAGCTGCTTTCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
gattgat putative branch site (score: 4)
ttatatgatacatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcctttcttgagagcttgagatttttcagctctttcttaaattaccttctgattgatgttgttatatgatacattcttatgtaagttgtgttctcttaaattgttaacagAGGGAGAGATATATTGTAACATATAACCCCTCAAAACACAAGGTTTATGCGGTGCTCAAGGATCAGGCAAAGTCAGATGACATTCTGAAAGCAGCATTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG