Sequence
atgc intronic sequence ATGC exonic sequence...tttgataggctatttggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaattgtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os03g01660.1 (Oryza sativa), 3'ss of exon 2
-------------------tttgatag--gctatttggttt--ttgttatatgatgtactcttattcact--ctttatc--cttttcttatggcctttatttattttgtttaaaattgtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
| ||| |||||| | | || || | | || || ||| | | ||||| || ||| | ||| ||||| ||| || | | | ||||| |||||| ||||| || ||||||||| || |||||||| || || |||||||||||||||||||| |||||||| ||||| |||
gtatgacccctatgcatttctagatcataactattttttctgtttattggaggggaaacaattgttctccagccttatcagctattcatttggttccaatttaatttcattgtgaactcacag-
upper sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G109725_T04 (Zea mays), 3'ss of exon 3
tttgataggctatttggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaattg--tgtatcaagA--TGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
|| || ||| | || |||| | || | |||| | || | || || | | || || | | ||| ||||||||||||| || ||||||||| ||||| ||||| || || |||||||| ||||| |||||||||||||| || |||||
----------------gtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
upper sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
------------tttgataggctatttggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaattg--tgtatcaagA--TGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
| || | ||| || ||| | || |||| | || | |||| | || | || || | | || || | | ||| ||||||||||||| || ||||||||| ||||| ||||| || || |||||||| ||||| |||||||||||||| || |||||
gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
upper sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G055785_T01 (Zea mays), 3'ss of exon 2
tttgataggctatttggtttttgttatatgatgtactcttattcact-ctttatccttttcttatggcctttatttattttgtttaaaattgtgtatcaagA----TGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
| ||| |||| || || ||||| | || || || | ||| | || | ||| || | ||| | ||||| | ||||||||||| || ||||||||| || |||||||| || || |||||||| ||||| |||||||||||||| | |||||
-gtaataaaaccagaggttca-attccctgcacccttcttagctgcaactccgctctgttaattcatcctatgttgagtttattggtggtgaactataatagGTGTTGAAGACATATATCTGGCTTCAGTGCTTTGATGGTTCCATACAACAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCAGGAAATTG---
upper sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G029307_T01 (Zea mays), 3'ss of exon 1
-------tttgataggctatttggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgttta-aaattgtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
|| || | || ||| | | | || | | | | |||| || | || ||||| || | ||| || || | || |||| ||||||||||||| || |||||| || || |||||||| || ||||| ||||||||||| ||||| |||||||| || ||||||
gtacattttccattgctgtttctgttaattagagaggaaatgttgtgttcttatcttcattgcatcatttgggcctaaatcaagttttttggtgaactctgacagGCATTGAAAACTTATATCTGGCTTCAGTGCTTTGATGGCTCCATACAACAAGTGGAGGAAGAAGTTGCCATGTTCTGCCCTATGATATGTCGGGAAATAA---
upper sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G30080.2 (Glycine max), 3'ss of exon 1
tttgataggctatt-tggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaatt--gtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
| | | || || ||| | ||| | | || || | | || ||| | | ||| || |||| | | || | | ||||||| || || |||||||| ||||||| |||||||||||||| ||||| || |||||||| ||||||||||||||||||||||||| ||| ||||||
--tatcgtgttgttctgaaatttacaacatggtaaagtcaagtttattgttgttccctgggtagctag-tttgttgatttcactctacctttggcatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATATGCCAGGAAGTACTTC
upper sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G25090.1 (Glycine max), 3'ss of exon 1
-tttgataggctatttggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaatt--gtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
| ||| ||| | || | ||| || | || || | | || | | | | ||| || |||| || || | ||||||| || || |||||||| ||||||| |||||||||||||| ||||| || |||||||| |||||||||||||||||||| |||| ||| ||||||
tacttctagattat--aatgattagaacatggtgaagtcaagtttattgttgttgcctgggtagctag-tttgttgatttcactttgcctttgccatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctttatccttttcttatggcctttatttattttgtttaaaattgtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
tttatttattttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgataggctatttggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaattgtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG