Sequence
atgc intronic sequence ATGC exonic sequence...gagatggtatctttgcatattcacagtttgcatgcttctaacacagatgacttgtttgccttaaagtataatataaaaattgaattaactgatgttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
Basic information
species | Glycine max |
transcript | GLYMA14G07850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g04020.1 (Oryza sativa), 3'ss of exon 3
gagatggtatctttgcatattcacagtttgcatgcttctaacacagatgacttgtttgccttaaagtataatataaaaattgaattaactgatgt-tgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
||| | | | | ||| | || | | || || || | | | | | ||| |||| | || ||||| | |||||||||| |||||| ||||||||||||||||| |||||| | ||||| | | |||||||| || || ||||| ||||||||| | |||
----------------gtatatataccctat-tacttaccat-catttttttaacccaactgcaaacatgctg--atgacttgactaattgatttgtgtagATTTCTAAAAGCAAGGAGATTTGACATTGAGAAAGCAAAGCAAATGTGGACTGACATGCTTAAATGGAGGAAGGAGTACGGTACAGATACAATTGTTGAG
upper sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g46720.2 (Oryza sativa), 3'ss of exon 2
-gagatggtatctttgcatattcacagtttgcatgcttctaacacagatgacttgtttgccttaaagtataatataaaaattgaattaactgatgttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
||| | ||||||| | || | | | | ||| | | | || ||| || || | | || ||| || || | || ||| | |||||| ||||||||||| |||||||||||||| |||||| | | ||| | | ||||| || |||| ||| |||| | ||| |||
agagtggcaatctttggagcagca-aatcattaagaggctaccctgaagaaaatgattggctggtcgtgtgaaattttcattttatctccttcacatatagGTTCCTCAAAGCACGGAAATTTGATGTTGAGAAAGCAAAGAGTATGTGGTCAGATATGCTTAAATGGAGAAAGGAATTTGGGGCTGACAA---TATAGAG
upper sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G171354_T03 (Zea mays), 3'ss of exon 3
-gagatggtatctttgcat----attcacagtttgcatgcttctaacacagatgacttgtttgccttaaagtataa-tataaaaattgaat-taactgatgttg-----cagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
| ||| | | || || ||| |||| | | | | | || || ||| | || | | | | | ||||| | || ||||| | |||||||||||||||||||| || ||||||||||| |||||| | ||| | || ||| ||| || ||||| |||||||| ||| |||||
gtatatgtatccagtaaattatgatgcaccttttgtttagct-tgatgtgttagttttcatttttccaaatcacaagtgcacagctcaagcctaactaaatctggtctttagATTTCTAAAAGCAAGGAAATTTGATATCGACAAAGCAAAGCAAATGTGGATGGATATGCTTCATTGGCGGAGGGAGTATGGCACTGATACGATTTTGGAG
upper sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G355610_T01 (Zea mays), 3'ss of exon 3
----gagatggtatctttgcatattcacagtttgcatgcttctaacacagatgacttgtttgccttaaagtataatataaaaattgaattaactgatgttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
| | | ||||| | || | ||| | | | | | || | ||| | | | | | | |||||||||| | |||||| ||||||||||| |||||||||| ||| | |||||| | ||||| | | |||||||| |||| || ||| | ||| |
gccacacacaaaa-ctttgtacatgtgc---ttgagaggccatgattggaagaaagtggtcgccatcctagttgactgggctgggattctcatttgcattgcagATTCCTAAAAGCACGGAAATTTGATGTTGAGAAAGCTAAGAATATGTGGTCAGACATGCTTAAATGGAGGAAGGAATTCGGGGTTGACAAAATAGAG---
upper sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G75370.1 (Arabidopsis thaliana), 3'ss of exon 2
--gagatggtatctttgcatattcacagtttgcatgcttctaacacagatgacttgtttgccttaaagtataatataaaaattgaattaactgatgttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
|||| ||| | || ||||| ||| |||| | | | | ||| | || || | | || || || |||| |||||||||||||| |||||||||||||||| |||| | ||| |||||| || |||||| | ||||| ||||| | ||||||||| || ||| | |||
gtgagactttatttctgtcgattcat--ttttcatgatgatgatgatggtgat------------gatgatgattttgatgttctatgttctc-tgtt--agATTCTTGAAAGCTAGGAAATTTGATATTGGGAAAACCAAGTTAATGTGGAGTAATATGATCAAATGGAGAAAAGATTTTGGTACTGACACCATTTTCGAG
upper sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 2
gagatggtatctttgcatattcacagtttgcatgcttc-taacacagatgacttgtttgccttaaagtataatataaaaattgaattaactgatgttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
| | | ||||| | ||| | | | |||| | | | | || | || | | ||| | ||||||||| |||||||| ||||| |||||||| || || || |||||||||||| || | ||||| |||||||||||| | | || || || || || |||||
--------------gtcttacaatgctttgcctttttcctgattttggctacttctctac---agagcttcattctcag---ggattg-ccatctttgcagATTTTTGAAAGCCAGGAAGTTTGATATGGAAAAGGCGAAGCACATGTGGACCGAAATGATTCACTGGAGGAAAAACTTCGGCACCGACACTATCTTGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgacttgtttgccttaaagtataatataaaaattgaattaactgatgttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
ttaaagtataatataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagatggtatctttgcatattcacagtttgcatgcttctaacacagatgacttgtttgccttaaagtataatataaaaattgaattaactgatgttgcagATTCTTGAAAGCAAGGAAATTTGATATTGAGAAAGCAAAGCACATGTGGGCCAACATGATCCACTGGAGGAAAGAATATGGTACTGATACAATTATGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA