Sequence
atgc intronic sequence ATGC exonic sequencegtaactgttatgcacgagtatacaaacactattaagcgatggttgatgatgaaaactctattaatccacgtggaatgctctaatttcatgtgcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG
Basic information
species | Glycine max |
transcript | GLYMA18G02960.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 3
--------gtaactgttatgcacgagtatac--aaacact---attaagcgatggttgatgatgaaaactctattaatccacgtggaatgctctaatttcatgtgcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG
| ||| ||| ||||| | || |||| |||| | || || || | | || | || ||| | || ||||| || |||||||| ||||| ||||| |||||||||||| | |||||||| || || || || || ||||||||||| |
gtacaaaatttgaagttttgccaaagtatgcgtaaccactttgtttaaattgtatcctataatcttaatgtattctttgcatattttattttcttttcacaatcacagGTTGTGTTTTGGAAATGGATCACCCCAAAGTTGTTGGGTTTGGTAACACAAACATCAGTTTATCACTGGTCAATTGAGG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 3
-------gtaa-ctgttatgcacgagtatacaaacactattaagcgatggttgatgatgaaaactctat-taatccacgtggaatgctctaatttcatgtgcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG---------------------
| || | || | | || | | || | ||| || || || | ||| || | | |||| ||||| || |||||||||||||| || ||||| ||||||||| | || ||||| || ||||| ||||| ||||| |||||||
gtacaaaacactctctgatactgttgcatcttgatgtttttctgtagctgttaattatatgcccttcaagtaacatgttctatatatttaatcttcaaccacagGTTGTATTTTGGAAGTGGATCACTCCCAAATTGTTGGGTTTAGTGACACAAACATCTGTTTACCACTGGTCGATTGAAGGTGATTCTGAGCCCACCAAGA
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaactgtt-atgcacgagtatacaaacactattaagcg--atggttgatgatgaaaact--ctattaatccacgtggaatgctctaatttcatgt-gcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG
|| | | || | ||| || ||| | |||| ||| | | | | || || | | | || ||| || | || || | |||| | |||||||||||||| || || ||| || |||| || || ||||| || ||||| || ||||||||||||||||
gtgaattttgaagcaaacaaattgtaacccgattatctttcatgttgtactcttcagacagactctgattttac-tggtctgaattttttggatattatagGTTGCTTTTTGGAAGTGGATCACACCTAAGATGCTGGGACTGGTCACACAAACTTCTGTGTATCATTGGTCAATTGAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaactgtt-atgcacgagtatacaaacactattaa-------gcgat-------ggttgatgatgaaaactctattaa---tccacgtggaatgctctaatttcatgt----gcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG
|| | |||| ||||| ||| ||| | |||| || || | | | |||| | | | | | | || | |||||||| ||||| |||||||||||||||||||| || ||| ||||||| || || ||||||| || || || ||||||||||||||||
gtgagtgttgatgcaaatatatttgaactccattatcgttcctgctatacacttcgtataactctgaatttttcagtcgggtttttttttggataataatgtttcatgtttttacagGTTGTCTTTTGGAAGTGGATTACACCAAAGATGTTGGGGCTGGTCACACAGAATTCCGTCTATCATTGGTCAATTGAAG
upper sequence: GLYMA18G02960.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtaactgttatgcacgagtatacaaacactattaagcgatggttgatgatgaaaact-ctatta-atccacgtgga--atgctctaatttcatgtgcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG
|| | || || | | | | |||| | || | || | || | | |||||| | | | | |||| | | | || | || || ||||||||||||||||| ||| || |||| || || || |||||||| ||||| ||||||||||| ||||
gtgagaactttgttctttagcatttctgttacatttcttgagc--tattttgacatcctacattgttaacattgctattacagttagcttaactatgccttgttgtttaaaatagATTGTTTTCTGGAAGTGGATTACCCCAAAGATGCTGGGCCTGGTCACGCAGACCTCAGTATATCATTGGTCAATCGAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttgatgatgaaaactctattaatccacgtggaatgctctaatttcatgtgcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG
aaaactctattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactgttatgcacgagtatacaaacactattaagcgatggttgatgatgaaaactctattaatccacgtggaatgctctaatttcatgtgcagGTGGTCTTTTGGAAGTGGATTACCCCCAAGTTGTTGGGTCTTGTAACACAGACCTCTGTATACCATTGGTCAATTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG