Sequence
atgc intronic sequence ATGC exonic sequencegttagttccctcaaatttctattccatttgatgaaattgtgtgtcttggatggatggattattgtaagtgattttgtttgttgttgcagTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC
Basic information
species | Glycine max |
transcript | GLYMA04G39500.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 1
gttagttccctcaaatttctattccatttgatgaaattgtgtgtcttggatggatggattattgt---aagtgattttgtttgttgttgc--agTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC
|| | || || ||| | ||| | |||| | | | || | | || | | ||| ||||| || | || || |||||||| ||||| || |||||||||||||||||||| |||||||| |||||
gtaacagccactgaacttc-accgttgttggtttttttgttccccattcggtagtaccttgtctcctcctgacatgtggattgctgttgtgaagCTCGCGGCGAGGATTGCGGTTTCCAACCTGCACAAGAACACCAAGAAGTCCTTCTCGGAGAC
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 1
----------------------------------gttagttccctcaaatttctattccatttga-tgaaattgtgtgtct-tggatggatggattattgtaagtgattttgtttgttgtt---gcagTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC
| | ||| | || || | || || || ||| | | || | || | ||| || | | | || || | || |||| || |||||||| || ||||| |||||||||||||| ||||| |||||||| |||||
gtgagtaacccaccccgaaatcctcctcccctctggccttggtttcagctctcctgtctgtctgtctgtctttctgtctgtgctgacgtggggttggttgcccctgttctctgtcgtgattcgtgaagCTGGCGGCGAGGATTGCTGTGTCGAACCTGCACAAGAACACAAAGAAGTCCTTCTCGGAGAC
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 1
----------------gttagttccctcaaatttctattccatttgatgaaattgtgtgtcttg--gatggatggattattgtaagtgattttgtttgttgttgcagTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC
| | ||| |||| | || | || |||| |||| || | || | | || | | | | || || ||||||| || |||||||| || || || |||||||||||||| ||||| |||||||| |||||
gtgaggaacccaccgtgaaatccccccttggtttcaactctcatgtctgtctttgt-tgtcctgacgtggggttggtttcctctcttctctatcgtgattcgtgaagTTGGCGGCGAGGATTGCTGTGTCTAACCTGCACAAGAACACAAAGAAGTCCTTCTCGGAGAC
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 1
--gttagttccctcaaatttctattccatttgatgaaattgtgtgtcttggatggatggattat-tgtaagtgattt-------tgtttgttgt-tgcagTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC
|| | | | || ||| ||| | || | | || | | || | | | | |||||| |||| | | | ||||||||||| ||||| | ||||| |||||||| |||||||| |||||||| || || |||||
tacttgaccgtcctttgtatggttttcatgggattcacaattgaagatacaagggtttgtttctattttaatgatttatgtgaccatttgatatgtacagTTGGCTGCAAGGATCGTTGTTTCAAATCTGCATAAGAACACAAAGAAATCATTTTCAGAGAC
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S195_46V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------------------------------------------------gttagttccctcaaatttctattcc---atttgatgaaattgtgtgtcttggatggatggattattgtaagtgattttgtttgttgttgcagTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC--------------------------------------
||| ||| || ||| | | | | | | | | || | | || | |||| | || | ||| |||| |||| || |||||||| || || ||| ||||||| |||||||||||||||||||| |||||
gtaagctgctcccacggcatggaccgttgtaattccgatagtttcagggccgtccattatttcactgtgattccaagttccgcactggtttctgctgatttagcttcccttccggccaagccgaagtaacttcttccactgt-gcagCTGGCGGCGAGGATTGCTGTCTCCAATTTGCACAAAAACACCAAGAAATCCTTCTCTGAGACTGTGAAGGATATGTATCGCCATGTGAACGCCAGATCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattgtgtgtcttggatggatggattattgtaagtgattttgtttgttgttgcagTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC
attattgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttccctcaaatttctattccatttgatgaaattgtgtgtcttggatggatggattattgtaagtgattttgtttgttgttgcagTTGGCTGCTAGGATTGCCGTTTCGAATCTGCACAAGAACACCAAGAAATCCTTCTCCGAGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA