Sequence
atgc intronic sequence ATGC exonic sequence...taattgaataatctgaactaagtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
Basic information
species | Glycine max |
transcript | GLYMA06G24890.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g44230.1 (Oryza sativa), 3'ss of exon 8
taattgaataatctgaactaagtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | | | || | || | || || |||| | || |||| | | | || ||| | || ||||||||| || || ||||||| ||| ||||| || ||||||||||| || |||||||| || |||||| | ||||| ||||||||| | ||| | | || |||
---gtacgtgacataaatt---ttcattctttgtaccttcagatatttcttcagttttttttttcg-----tatgttatgacactaccacctgtaaacagGTTGCTCGGAAAATGAGAGAGGAGGATGGATTTTATTATCCCCATAATCTTGATTTTCGTGGCCGTGCATACCCTATGCATGCACATCTAAGCCACCTAG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G115564_T01 (Zea mays), 3'ss of exon 8
taattgaataatctgaactaa-gtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | | || || | |||| | | | ||||| | || | | | || | || | | ||| | |||||||| || || ||||||| ||| ||||| || |||||||| || |||||| | || |||||||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataaatactgttcattcttgc-tgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G370326_T01 (Zea mays), 3'ss of exon 7
taattgaataatctgaactaa-gtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | | || | || |||| | | | ||||||| || | ||| || | || | | ||| | |||||||| || || ||||||| ||| ||||| || |||||||| || |||||| | || ||| |||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataattattgttcattcttgc-tgagatactatggtgcagtttatatgttattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCTGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G440258_T01 (Zea mays), 3'ss of exon 5
taattgaataatctgaactaa-gtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | | || | | |||| | | | |||| | || | | | || || || | | ||| | |||||||| || | ||||||| ||| ||||| || |||||||| || |||||| | || |||||||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataattactgttcattcttgc-tgagataccgtggtgcagtttatatgctattacattgttggaattatacttgttccttttctgtaaacagGTTGCTCATAAAATGAGAGAGGAGGATGGATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G528717_T01 (Zea mays), 3'ss of exon 5
taattgaataatctgaactaa-gtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | | || | | |||| | | | ||||| | || | | | || | || | | ||| | |||||||| || || ||||||| ||| ||||| | |||||||| || |||||| | || |||||||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataattactgttcattcttgc-tgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTAGATTTCCGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G133353_T01 (Zea mays), 3'ss of exon 3
taattgaataatctgaactaagtttac-cattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaa----tacattct---taaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | | || | || |||| | | | ||||| | || | | | || | || | | | |||| | ||||||||| || || ||||||| ||| ||||| | |||||||| || |||||| | || ||| |||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataattactattcattcttgc-tgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttcattttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTAGATTTCTGTGGGCGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G319000_T01 (Zea mays), 3'ss of exon 4
taattgaataatctgaactaa-gtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattctt-------aaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | | || | | |||| | | | ||||| | || | | | || | || | | ||| | |||||||| || || ||||||| ||| ||||| | |||||||| || |||||| | | |||||||| | ||||| ||||||||||||||||||| ||| |||
---gtatgcagcataaataattactgttcattcttgc-tgagatactgtggtgcagtttatatgctattgcattgctggaattatacttgttccttttctgtaaacagGTTGCTCGTAAAATGAGAGAGGAGGATGAATTTTATTACCCTCACAATTTATATTTCCGTGGGTGTGCATACCCTATGCATCCTCATTTGAGTCACCTAG
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G24120.2 (Arabidopsis thaliana), 3'ss of exon 8
taattgaataatctgaactaagtttaccattatcacattcaatact--atcccatgtttcactagttgagcaataatttaaaggaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
| | || | | ||| | | | | | || | || || | | || || || | ||| || | |||||||| |||||||||| || || ||||| || || || || |||||||||||||| | ||| | ||||| || |||||||||||| |||||||| |
--------------gtaagaaatacattcttactgcttaagacttttcgttccgtcttcacttaactaggaaaagatatagactaaaggttatcattg-cagGTGGCTAGAAAAATGAAGGACGAAGAAGGATTCTACTACCCTCACAATCTTGACTTTAGAGGCCGTGCATACCCAATGCATCCTCATCTGAATCATCTGA
upper sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 8
taattgaataatctgaactaagtttaccattatcacattcaatactatcccatg-tttcactagtt---gagcaataatttaaaggaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
|| |||| | | || ||| || | | || | || | || ||| | | ||| | || |||| || |||||||||| ||||||||||||||||| ||||||||||||||||| ||||||||||| || || ||| | || || || |||||||| |||||||||||| |
---tttcctaatgcagatttgattatgtattgccatgactggaagtctcgaagaactttgttcatttgtaagcttcagtgctaagcagattcatt-ttgaacagGTGGCTCGAAAAATGAAAGATGAAGAAGGCTTTTATTATCCTCACAATCTTGATTTTCGAGGCCGTGCGTACCCAATGCATCCACATTTGAATCATCTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcccatgtttcactagttgagcaataatttaaaggaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
cattctt CT-rich tract
aataatttaaaggaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taattgaataatctgaactaagtttaccattatcacattcaatactatcccatgtttcactagttgagcaataatttaaaggaaatacattcttaaacagGTGGCACGAAAAATGAAAGATGAGGAAGGCTTTTATTATCCACACAATCTTGACTTCCGTGGCAGAGCATATCCTATGCATCCTCATTTGAATCATTTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - -tctgaac
- - - - - - - - - - - - - - - - - acattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaatac