Sequence
atgc intronic sequence ATGC exonic sequence...actatttgtgcgtcatgttatgattgtttataatatcagaatatgtcaatgctttctgaacatgtgctgatttaactatacttatacttcatattgtcagCTTGGATACACCAAAAAACAAGAAGAGAGACATTTCCGAGGAGTAATTACGTTAGAG
Basic information
species | Glycine max |
transcript | GLYMA07G40300.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 15
----------------------------------------------------------actatttgtgcgtcatgttatgatt-gtttataatatcagaatatgtcaatgctttctgaacatgtgctgatttaactatacttatacttcatattgtcagCTTGGATACACCAAAAAACAAGAAGAGAGACATTTCCGAGGAGTAATTACGTTAGAG
| | || || | || || | ||| | | || | ||| | | | | || || || | | || || | || || |||||||| |||||||| |||||||| ||||||||||| ||||| || ||| | |||
gttaatatatctcgtacactgatgtactggtgttccccatatttgatttttctgaataataacttatg-ataatcttgtcatttgctgccgattttcaaatgtcctttatttagttaagaatttggtg--tcatttactgttttttttttcatgtccagCTTGGGTACACCAAGAAACAAGAGGAGAGACATTTTCGAGGTGTTATTGTCCTGGAG
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G485898_T02 (Zea mays), 3'ss of exon 15
actatttgtgcgtcatgttatgattgtttataatatcagaata--tgtcaatgctttctgaacatgtgctgatttaactatacttatacttcatattgtcagCTTGGATACACCAAAAAACAAGAAGAGAGACATTTCCGAGGAGTAATTACGTTAGAG
|| | || | | || | |||| || || | || | | ||| | || | || || | | || | | |||||||||||||| || |||||||| ||||||||||| || || ||
------------------gttggtagtat-cagcattaaaatactcatccattcctttt-accattta-tggtgcctcttaacatttgttttgtg--gccagCTTGGATACACAAAGAAACAAGAGGAGAGACATTTTCGGGGTGT-------------
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 15
actatttgtgcgtcatgttatgattgtttataatatcag--aatatgtcaatgctttctgaacatgtgc-tgatttaactatacttatacttcatattgtcagCTTGGATACACCAAAAAACAAGAAGAGAGACATTTCCGAGGAGTAATTACGTTAGAG
|| ||| | | | || ||| | |||| | | | | | | | || || || |||| | | | | || | || ||| ||||||||||| ||||||||||||||||| |||||||| || || || |||| || |||
-tgatgtgtttttattttcatatttgccactgatatttgctatttttttagaattacttgtttatatgtgtgatatgtttg-atgtcgaccttattttg-cagCTTGGATATACCAAAAAACAAGAAGAAAGACATTTTCGTGGTGTTATTAATTTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaatgctttctgaacatgtgctgatttaactatacttatacttcatattgtcagCTTGGATACACCAAAAAACAAGAAGAGAGACATTTCCGAGGAGTAATTACGTTAGAG
atttaac putative branch site (score: 3)
atttaactatacttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
actatttgtgcgtcatgttatgattgtttataatatcagaatatgtcaatgctttctgaacatgtgctgatttaactatacttatacttcatattgtcagCTTGGATACACCAAAAAACAAGAAGAGAGACATTTCCGAGGAGTAATTACGTTAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - tttgtgc
- - - - - - tcatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat