Sequence
atgc intronic sequence ATGC exonic sequence...gtgtgtgtttacgtgtgagagaatgaactcttagttggcatagtatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
Basic information
species | Glycine max |
transcript | GLYMA20G36070.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g10770.1 (Oryza sativa), 3'ss of exon 6
---------gtgtgtgtttacgtgtgagagaatgaactcttagttgg----catagtatctttagttttgataac-----agctttatattttctttgt--ggtttaattatggatgc----agCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
|||| || | ||| | | | |||||| | | | ||| || ||| | | | | |||| | || ||||| | | ||||||| ||||| ||||||||||| ||| | || ||| |||||||||| || ||||| |||||||||| || || ||||| ||||| || ||||||
gtaagatgcttgtgatattgcttgtcatgactttctgttctagttgtgcttcttgattcttttttttcccgaaactatccaacctgagatttgttacactcaattgtgttatgtctactaacagCATGTTGAAGACCATCATTTATACTCACTAAACTACATGCATTGGGGTGCCCCAAAGTTGTGGTATGGAGTTCCAGGAAAGGATGCTGTGAATTTGGAAT
upper sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G156910_T01 (Zea mays), 3'ss of exon 6
----------------------------------gtgtgtgttt-acgtgtgagagaatgaactcttagtt---ggcatagtatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
|| |||| || | | || ||| | ||| || | | ||| | | | | |||| || | | | ||| | || || || |||||||| |||||||||||||| || ||| |||| ||| |||||||||| |||||||| ||||||||||| || || || || ||||| || ||||| |
gtaagatgcttttgatattctctttagtttcatagtttgtggttgatgctattgattatggaagctttattatggacttagggtatcca-tcttga-aatatttcactgatttgaatttgaattgtgcctgttgacagCATGTTGAAGATCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGGAAGGATGCTGTGAATTTGGAGG
upper sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G027075_T02 (Zea mays), 3'ss of exon 6
-------------gtgtgtgtttacgtgtgagagaatgaactcttagttggcatagtatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
| ||| ||| | | | || || | |||| ||| |||| | || || | | | ||| ||| | | || |||||||| ||||| |||||||| || ||| |||| ||| |||||||||| |||||||| ||||||||||| || || ||||| |||||| || ||||| |
gtaagatgcttgttggcatgtctacttctcttaccattaatatt--gttgtcat--tatccaaatttaacattcatgttctgagattttacactggcatgtctctgctgacagCATGTTGAAGACCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGAAAGGATGCCGTAAATTTGGAGG
upper sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G140524_T02 (Zea mays), 3'ss of exon 7
-------------gtgtgtgtttacgtgtgagagaatgaactcttagttggcatagtatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG-
| ||| ||| | | | ||| || | |||| ||| |||| | || || | | | ||| ||| | | || |||||||| ||||| |||||||| || ||| |||| ||| |||||||||| |||||||| ||||||||||| || || ||||| ||||| || ||||| | ||
gtaagatgcttgttggcatgtctacttctcttacaattaagatt--gttgtcat--tatccaaatttaacattcatgttctgagattttacactggcatgtctctgctgacagCATGTTGAAGACCATCATTTGTACTCACTGAACTACATGCATTGGGGTGCTCCAAAGATGTGGTATGGAGTTCCAGGAAAGGATGC-TGTAAATTTGGAGG
upper sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G08620.2 (Arabidopsis thaliana), 3'ss of exon 7
gtgtgtgtttacgtgtgagagaatgaactcttagttggcatagtatcttt-agttttgataacagctttat---attttctttgtggtttaatta--tggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
| | | | | | | ||||| || | | ||| || | || ||| | ||| | ||| ||| || ||| || || ||||||| |||||||| || || ||||| |||||||| |||| ||||| || || ||| ||||||||||||| || || ||||| ||| | || |
------atgcaattttcattacttcacatcttatttcgttttatattttccacttctgacattccttttgttctgctttttttttgtttttgtttacctgaaatagCATGTTGAAGATCACCACTTGTATTCGTTGAATTATATGCACTGGGGTGCACCGAAATTGTGGTATGGTGTTGGGGGGAAGGATGCTGTTAAACTCGAGG
upper sequence: GLYMA20G36070.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0036g00570.t01 (Vitis vinifera), 3'ss of exon 8
-gtgtgtgtttacg-tgtgagagaatgaactcttagttggcatagtatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
|| | | | || | | ||| ||| | | | || | ||| ||| | ||||| | || ||| |||| || || |||||||| ||||||||||| |||||||| ||||| ||| |||| ||||| ||||||||||| |||||||||||||| || |||||||| |||||||| |
agtatttaatgacacttttagatgttgattatgctgattcttttgtttatttg--tttatttgtttatttatttattttttcaaatttatttttgagaacagCATGTTGAAGATCATCACTTATATTCGTTGAACTACATGCACTGGGGTGCTCCAAAAATTTGGTATGGTGTCCCAGGGCAAGATGCCCTTAAATTGGAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
tttatattttctttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgtgtttacgtgtgagagaatgaactcttagttggcatagtatctttagttttgataacagctttatattttctttgtggtttaattatggatgcagCATGTGGAAGATCATCATTTATATTCATTGAATTACTTGCATTGGGGAGCTCCAAAAATGTGGTATGGTGTCCCTGGAAAAGATGCCTGCAAATTGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
gtgtgtg
- - - - - acgtgtg
- - - - - - - - - - -aatgaac