Sequence
atgc intronic sequence ATGC exonic sequencegttagtattcttgttgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
Basic information
species | Glycine max |
transcript | GLYMA07G38050.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 11
gttagtattcttgttgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|||| || ||| || | | |||| || | ||| ||| || ||| ||| || |||| || || || | |||||| || |||| ||| ||||||||||| || ||||| |||||||| ||||| ||||||||||||||||||||||||||||||||||||
----gtatgct-gttatgtgcaaattgttttct--tctgaacccatga-atatgt--atgttgaatatttagtgttaatg--tgttgatgtcttcagGAATCCACAAGCTGATCTGCAAGCTCAAGACCGTGCACATAGGATAGGTCAGAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 11
gttagtattcttgttgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|| | | || | ||| || | || | | || || ||| ||| | | || || | | | | ||||||| |||||||| || |||||||| || |||||||| ||||| ||||||||||||||||||||||||||||| || || |||||||||
------------gtatgtccttttcaaa-tcgtaattttttctcattctacaa-tttgtgaa-----gttaaaggttatggttatttggtttcacagGAATCCTCAAGTGGATCTGCAAGCGCAAGATCGTGCACATAGAATTGGTCAAAAGAAAGAAGTTCAAGTTTTTCGTTTCTGCACTGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 11
gttagtattcttgt-tgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|| ||| | || | | || | | || |||| ||||| | | |||| | | ||| | |||||| || |||| ||| |||||||||||||| ||||| |||||||| ||||||||||||||||||||||| ||||| ||||||||||||
------------gtatgagactatgctaaacttgattctgttgct-taccctaagaatgaatctaat-gcctctgttatt--tctgtgcctc---cagGAATCCACAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGGATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 8
gttagtattcttgttg-attgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|| | ||||| | || || | ||| | ||| | ||||| | | | || | || || || |||||| || |||| ||| |||||||||||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||||||||||
gtatgcgactttgttatgctaaatttagttttgttgcttataccctaagcatgaagccatga--accttatgttcctagtactt--ctgtgcctccagGAATCCCCAAGCTGATCTGCAAGCTCAGGACCGTGCACATAGAATAGGTCAAAAGAAAGAAGTTCAAGTGTTCCGCTTTTGCACTGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 11
gttagtattcttgttgattgtcagcagccttcta-acttgcagtgatgccataagttcatgactaattgtttttgttgataattggtgg-ttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|| || | || | || || || ||| | | || | | ||| | ||||| |||| ||||||||||||||||||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| || ||||| |||
-------------------gtaaggctctttttgtgtccattgtaat-ttatgagtgttttctt--ttatgcctaatga-ggtgggtggattatggcagGAACCCTCAAGTTGACTTGCAAGCTCAGGATCGTGCACATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTCCGGTTCTGCACCGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: AT3G06400.3 (Arabidopsis thaliana), 3'ss of exon 11
gttagtattcttgttgattgtcagcagccttctaacttgcagtgatgcc-ataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|| || | | | || || | || | | || | |||| || | | || | ||||||||| ||||| ||| ||||||||||||||||||| ||||||||||||||||| |||||||||||||| || ||||| |||||||||
-------------------gtaagtctctcatcattgtccactgtagtttatgaactt---tctcttcacgtttgacgagtctggcatattctggcagGAACCCACAAGTCGACTTGCAAGCTCAGGATCGTGCCCATAGGATTGGTCAAAAAAAAGAAGTTCAAGTGTTTCGATTCTGCACTGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 11
gttagtattctt--gttgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|| || ||| | || || | ||| || ||| | | | || | | | | | |||||| | | |||||||| |||||||| ||||||| || |||||||||||| |||||||||||||||||||||||||||| || ||||| ||||| |||
gtgagcatttctccatttttttttctttttcttttagaatgctagggaattgt---tatattatttaccaatctggttgatctctttattgcaccgtagGAACCCCCAAGTTGATTTGCAAGCACAAGATCGTGCTCATCGGATTGGTCAAAAGAAAGAAGTTCAAGTGTTTCGATTCTGCACAGAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 11
gttagtattcttgttgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|| || | || | | | | | | || | || | || | |||||| |||||||| || ||||||| || ||||| || ||| ||||||| || || ||||||||||||||||||||||||||||| ||
-----------------------------------------gtaataataatgatttgttctgagtggcatgtttttagaaattatgct----gcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG
upper sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 11
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 11
gttagtattcttgttgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
|| || | || | | | | | | || |||| | |||||| |||||||| || ||||||| || ||||| || ||| ||||||| || || ||||||||||||||||||||||||||||| ||
-----------------------------------------gtaatagtaatgatttgttctgagtggcatgttttagaaatta-----tgctgcagGAATCCTCAAGTCGATTTGCAAGCGCAAGATCGAGCACATCGGATTGGACAGAAAAAAGAAGTTCAAGTTTTCCGATTTTGCACGCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
taattgtttttgttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtattcttgttgattgtcagcagccttctaacttgcagtgatgccataagttcatgactaattgtttttgttgataattggtggttataacagGAACCCTCAAGTTGACCTGCAAGCTCAGGATCGTGCTCATAGGATTGGTCAAAAGAAAGAAGTTCAAGTTTTCCGATTTTGCACTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT