Sequence
atgc intronic sequence ATGC exonic sequence...aatttattccttgagcttgctattagcttgatagttaccagtatactgtcatggacaccctaattactgtaatctattgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA
Basic information
species | Glycine max |
transcript | GLYMA05G13920.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os10g30100.1 (Oryza sativa), 3'ss of exon 6
----------------------------aatttattcct-tgagcttgctattagcttgatagttaccagta-tactgtcatggacaccctaattactgtaatctattgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA---
||||| | || | | || ||| | || | | || | | | | | ||| || ||||| || || || ||||| ||||||||||||||||||||||| |||||||||||||| ||||| | | | | | || ||||| || | | |
gtagactacctttctgaaacccctcatgaatttccttctatttccatgttatacatccactttttgtcgatggctctactctcgctgatcatttccatcaaatgtacctgattatgccttctttgtttagGTATGCTAGAGAAGATACACATTATCTGCTTTACATATATGATTTGATGAGACTCAGACTGGTGAAAGAGTCTTCAGA---TGAAAATGATCTTCTTTTAGAG
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 6
aatttattccttgagcttgctattagcttgatagttaccagtatactgtcatggacaccctaattactgtaatctat---tgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA---
|| || ||| | ||| | || | | | || | | | || | | | | || | | | ||| | | | | | || ||| ||||| |||||||||||||| |||||| | |||||||||||||| ||||| | ||| | | | | ||||| || | || |
-tcttttttattgtgtttggtgttggat-attttttgtttgcttcttttcttt-atttctgacttgccatcagttatatataagtggctttacttctgcccagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGATTTAATGAG-ACAGAG--ACTACAGAGGGAGTCAACATTTGAAAATGATCTTCTTCTAGAG
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G118917_T02 (Zea mays), 3'ss of exon 6
-----------------------aatttattccttg--agcttgctattagcttg-atagttaccagtatactgt---catggacaccctaattactgt--aatctattgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA---
||| ||| | || | || |||| || || || | | | | || || | | ||||| | | | ||| ||| | ||| | ||||||||| ||||| |||||||| ||||||||||| |||||||| | ||||| |||||| | | ||| | | | ||||| || | | |
gtactgtgcattgatactctgtccattgatttcatgtttgtttaatatttctttttatcattttccattttccgtcctcacccagagaataatttccaccaagtgtatctcattgtgattgctgtgtgcagATATGCTAGAGAGGATACACACTATCTGCTATATATATATGACCTGATGAG-ATTGAGAC-TAGTGAATGGGTCATCA-TGTGAAAATGATCTTCTTTTAGAG
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 6
----------------------------------aatttattccttgagcttgctattagcttgatagttaccagtatactgtcatggacaccctaattactgtaatctat---tgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA
|| ||||| ||| | || | | | | | | || | || | || | | | ||| | | | | | || || ||||| |||||||||||||| |||||| | ||||||||||| || ||||| | ||
gtattgtgcatataccctattctgaatttcttttctgttgactgttgagtttggtgttggatatttttgtgtttgc-tgcttttattttttgctggcttgccatcagttatatataagtggatttacttctgcctagGTATGCTAGAGAAGATACACACTATCTGTTGTACATATATGACTTAATGAGACAGGCCCTA---------------------------------------
upper sequence: GLYMA05G13920.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 6
aatttattccttgagcttgctattagcttgatagttaccagtatactgtcatggacacccta-attactgtaatctattgaatta--ttattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA
|||| | | | | || ||||| | | ||| | | | | || || | | ||| ||||||||| |||||||||||||||||||| | ||||| |||||| | ||| | || ||||| | ||| ||||| ||| |||| ||||
---------------------gttagtatattctctgtctagtctctctcatgattgctttgcattggttgagttgagctaacacatttgcatataatggcagATATGCTAGAGAAGATACACATTATCTTTTGTACATTTATGATGTAATGCGAATGGAGTTGCACACAATGGCAAAGGAAGATGAGCAATCTGACTCTCCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgtcatggacaccctaattactgtaatctattgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA
ccctaat putative branch site (score: 3)
ttatttttt putative PPT
taattactgtaatcta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttattccttgagcttgctattagcttgatagttaccagtatactgtcatggacaccctaattactgtaatctattgaattattattttttatgacagATATGCCAGAGAAGATACACATTATCTGCTATACATATATGATTTCATGAGGATTGAGTTATTTTCCATGCTTAAGGAGCCTGAAAGTGTTGACGCTCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - ttccttg
- - - - - - - gcttgct
- - - - - - - - - - - - - - - - - - - - - -tactgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gacaccc