Sequence
atgc intronic sequence ATGC exonic sequencegtatccagttaatttcatttctatatagtaatgtgtgtctgcacatttggttaaaatgacaggatggagtattgatgctatattaattttcagCATAAGCCGATGTCAGAAATTACTTCTGGTTTGCATCGTGGAATATATCATCAAGGGAAACTTCGTGTTAACCGTTATAATCCATTTGAAGCATATGTTG
Basic information
species | Glycine max |
transcript | GLYMA04G39980.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g03710.1 (Oryza sativa), 3'ss of exon 6
gtatccagttaatttcatttctatatagtaatgtgtgtctgcacatttggttaa--aatgacaggatggagtat-tgatgctatattaat-tttcagCATAAGCCGATGTCAGAAATTACTTCTGGTTTGCATCGTGGAATATATCATCAAGGGAAACTTCGTGTTAACCGTTATAATCCATTTGAAGCATATGTTG
| |||| ||||| | | | | ||| | |||| | | | || || ||| | || | || || ||||| || || |||||||||||||| |||| ||| ||||||| |||||||||||||| || || ||||| ||||| |||||||||||||| || ||||
--gtacagtaaatttaaactgttgacttgtgcttgttttattggcgttggccatctagtatcaaatacgaatatgtaatttcttgctatcattgcagCACAAACCTATGTCAGAAATTACAGCTGGCCTGCGGTGTGGAATTTATCATCAAGGGAAGCTCCGAGTTAATCGTTACAATCCATTTGAAGCTTACGTTG
upper sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G031859_T01 (Zea mays), 3'ss of exon 6
gtatccagttaatttcatttctatatagtaatgtgtgtctgcacatttggttaaaatgacaggatggagtattgatgctatattaattttcagCATAAGCCGATGTCAGAAATTACTTCTGGTTTGCATCGTGGAATATATCATCAAGGGAAACTTCGTGTTAACCGTTATAATCCATTTGAAGCATATGTTG
|||| | || | | | | ||| | | ||| ||| | ||||| || | || | ||||| || ||||| || || |||||||||||||| |||||||||| ||||||| || ||||||||||| ||||| ||||| ||||| ||||| |||||||| |||||||
gtatgctaactatacagtagtgcttttttgatg-acatatacactcttgcgtgaaatgtactcatc---tgtttgtttggtatta--ttacagCACAAACCTATGTCAGAAATTACATCTGGTTTGCGGTGTGGAATCTACCATCAAGGGAAGCTTCGAGTTAATCGTTACAATCCGTTTGAAGCTTATGTTG
upper sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G17510.2 (Arabidopsis thaliana), 3'ss of exon 7
-------gtatccagttaatttcatttctatat-agtaatgtgtgtctgcacatttggttaaaatgaca---ggatggagtattgatgctatattaattttcagCATAAGCCGATGTCAGAAATTACTTCTGGTTTGCATCGTGGAATATATCATCAAGGGAAACTTCGTGTTAACCGTTATAATCCATTTGAAGCATATGTTG
|| | | || |||| | | || || || || | | | | ||| || | | | ||| | | | | ||||||||||| ||||| || |||||| |||| || || |||||||||||||||||||| ||||| || || || |||| ||||| | ||||| |||||||
gtaatggagataaacacatttgtttttcagtctcagctttgggtaacttgatactgccatcaaacaacttttatctccaattttgttttttttcctgcctgcagCATAAGCCCATGTCTGAGATTACTGCTGGCTTACACCGTGGAATATATCATCAAGGAAAACTCCGGGTCAATCGTTTCAATCCTTACGAAGCTTATGTTG
upper sequence: GLYMA04G39980.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g02190.t01 (Vitis vinifera), 3'ss of exon 6
gtatccagttaatttcatttctatatagtaatgtgtgtctgcacatttggttaaaatgacaggatgg-------agtattgatgctatattaattt--tcagCATAAGCCGATGTCAGAAATTACTTCTGGTTTGCATCGTGGAATATATCATCAAGGGAAACTTCGTGTTAACCGTTATAATCCATTTGAAGCATATGTTG
| || | | || ||||| || || | | ||||| | ||| ||| | | || |||| |||| ||| ||||||||||| ||||| || |||||||||||||||||||||||||| || |||||||| ||||| || ||||| || || ||||| ||||||||||||||||
-cagaatgtgcccctatctgagattaggtaatatgggttttc-tatttgcatgaaacattgttgtggctttacaaattttcttgctttattgttttgtccagCATAAGCCCATGTCTGAGATTACTTCTGGTTTGCATCGTGGAATCTACCATCAAGGAAAACTACGGGTTAATCGCTACAATCCTTTTGAAGCATATGTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgcacatttggttaaaatgacaggatggagtattgatgctatattaattttcagCATAAGCCGATGTCAGAAATTACTTCTGGTTTGCATCGTGGAATATATCATCAAGGGAAACTTCGTGTTAACCGTTATAATCCATTTGAAGCATATGTTG
tattaat putative branch site (score: 2)
ttttc CT-rich tract
tattgatgctatatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatccagttaatttcatttctatatagtaatgtgtgtctgcacatttggttaaaatgacaggatggagtattgatgctatattaattttcagCATAAGCCGATGTCAGAAATTACTTCTGGTTTGCATCGTGGAATATATCATCAAGGGAAACTTCGTGTTAACCGTTATAATCCATTTGAAGCATATGTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC